Sample records for choanoflagellate monosiga brevicollis

  1. The early evolution of the phosphagen kinases--insights from choanoflagellate and poriferan arginine kinases. (United States)

    Conejo, Maria; Bertin, Matt; Pomponi, Shirley A; Ellington, W Ross


    Arginine kinase (AK) is a member of a large family of phosphoryl transfer enzymes called phosphagen (guanidino) kinases. AKs are present in certain protozoans, sponges, cnidarians, and both lophotrochozoan and ecdysozoan protostomes. Another phosphagen kinase, creatine kinase (CK), is found in sponges, cnidarians, and both deuterostome and protostome groups but does not appear to be present in protozoans. To probe the early evolution of phosphagen kinases, we have amplified the cDNAs for AKs from three choanoflagellates and from the hexactinellid sponge Aphrocallistes beatrix and the demosponges Suberites fuscus and Microciona prolifera. Phylogenetic analysis using maximum likelihood of these choanoflagellate and sponge AKs with other AK sequences revealed that the AK from the choanoflagellate Monosiga brevicollis clusters with the AK from the glass sponge Aphrocallistes and is part of a larger cluster containing AKs from the demosponges Suberites and Microciona as well as basal and protostome invertebrates. In contrast, AKs from Codonosiga gracilis and Monosiga ovata form a distinct cluster apart from all other AK sequences. tBLASTn searches of the recently released M. brevicollis genome database showed that this species has three unique AK genes-one virtually identical to the M. brevicollis cDNA and the other two showing great similarity to C. gracilis and M. ovata AKs. Three distinct AK genes are likely present in choanoflagellates. Two of these AKs display extensive similarity to both CKs and an AK from sponges. Previous work has shown CK evolved from an AK-like ancestor prior to the divergence of sponges. The present results provide evidence suggesting that the initial gene duplication event(s) leading to the CK lineage may have occurred before the divergence of the choanoflagellate and animal lineages. PMID:18064398

  2. The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

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    Manuel Michaël


    Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

  3. Narrower bottlenecks could be more efficient for concentrating choanoflagellates (United States)

    Sparacino, J.; Miño, G.; Koehl, M. A. R.; King, N.; Stocker, R.; Banchio, A. J.; Marconi, V. I.


    In evolutionary biology choanoflagellates are broadly investigated as the closest living relatives of the animal ancestors. Under diverse environmental cues, choanoflagellate Salpingoeca rosetta can differentiate in two types of solitary swimming cells: slow and fast microswimmers. Here we present a first phenomenological 2D-model for the choanoflagellates dynamics confined into a flat device divided by a wall of asymmetric microconstrictions. The model allow us to optimize the geometry of the microchannels for directing and concentrating cell populations under strict control. We solve our set of dynamical equations using Langevin dynamics. Experimental parameters for the motility of the slow and fast cells were measured and used for our numerical estimations of the directed transport efficiency, otherwise we have no adjustable parameters. We find remarkable differences in the rectification results for slow and fast choanoflagellates, which give us a strategy to develop a suitable microfluidic sorting device. For a given population velocity, narrower bottlenecks, of similar size to the cell dimension, show to be more efficient as concentrator of populations. Experiments and simulations are in good agreement.

  4. Gene : CBRC-MEUG-01-2461 [SEVENS

    Lifescience Database Archive (English)


  5. Non-systemic fungal endophytes in Carex brevicollis may influence the toxicity of the sedge to livestock

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    Rosa M. Canals


    Full Text Available The sedge Carex brevicollis is a common component of semi-natural grasslands and forests in temperate mountains of Central and Southern Europe. The consumption of this species causes a severe toxicity to livestock, associated to high plant concentrations of the β-carbolic alkaloid brevicolline. This research was started to ascertain the origin of this toxicity. An exploratory survey of alkaloid content in plants growing in contrasting habitats (grasslands/forests did not contribute to find a pattern of the variable contents of brevicolline in plants, and led us to address other possibilities, such as a potential role of fungal endophytism. Systemic, vertically-transmitted endophytes producers of herbivore-deterrent alkaloids are known to infect many known forage grasses. We did not detect systemic endophytes in C. brevicollis, but the sedge harboured a rich community of non-systemic fungi. To test experimentally whether non-systemic endophytes influenced the synthesis of the alkaloid, 24 plants were submitted to a fungicide treatment to remove the fungal assemblage, and the offspring ramets were analysed for alkaloid content. Brevicolline was the major β-carbolic alkaloid detected, and the contents were at least five times lower in the new ramets that developed from fungicide-treated plants than in the untreated plants. This result, although not conclusive about the primary source of the alkaloid (a plant or a fungal product indicates that fungal endophytes may affect the contents of the toxic brevicolline in this sedge.

  6. Phylogenetic relationships of the intercellular fish pathogen Ichthyophonus hoferi and fungi, choanoflagellates and the rosette agent

    DEFF Research Database (Denmark)

    Spanggaard, Bettina; Skouboe, P.; Rossen, L.; Taylor, J.W.


    18S rRNA sequences indicate that I, hoferi is not a member of the Fungi. In both the parsimony and the neighbor-joining trees, I, hoferi is the sister taxon to the rosette agent. The clade encompassing I. hoferi and the rosette organism is the sister group to the choanoflagellate clade in the...

  7. Phylogenetic Analysis of the Teneurins: Conserved Features and Premetazoan Ancestry (United States)

    Tucker, Richard P.; Beckmann, Jan; Leachman, Nathaniel T.; Schöler, Jonas; Chiquet-Ehrismann, Ruth


    Teneurins are type II transmembrane proteins expressed during pattern formation and neurogenesis with an intracellular domain that can be transported to the nucleus and an extracellular domain that can be shed into the extracellular milieu. In Drosophila melanogaster, Caenorhabditis elegans, and mouse the knockdown or knockout of teneurin expression can lead to abnormal patterning, defasciculation, and abnormal pathfinding of neurites, and the disruption of basement membranes. Here, we have identified and analyzed teneurins from a broad range of metazoan genomes for nuclear localization sequences, protein interaction domains, and furin cleavage sites and have cloned and sequenced the intracellular domains of human and avian teneurins to analyze alternative splicing. The basic organization of teneurins is highly conserved in Bilateria: all teneurins have epidermal growth factor (EGF) repeats, a cysteine-rich domain, and a large region identical in organization to the carboxy-half of prokaryotic YD-repeat proteins. Teneurins were not found in the genomes of sponges, cnidarians, or placozoa, but the choanoflagellate Monosiga brevicollis has a gene encoding a predicted teneurin with a transmembrane domain, EGF repeats, a cysteine-rich domain, and a region homologous to YD-repeat proteins. Further examination revealed that most of the extracellular domain of the M. brevicollis teneurin is encoded on a single huge 6,829-bp exon and that the cysteine-rich domain is similar to sequences found in an enzyme expressed by the diatom Phaeodactylum tricornutum. This leads us to suggest that teneurins are complex hybrid fusion proteins that evolved in a choanoflagellate via horizontal gene transfer from both a prokaryotic gene and a diatom or algal gene, perhaps to improve the capacity of the choanoflagellate to bind to its prokaryotic prey. As choanoflagellates are considered to be the closest living relatives of animals, the expression of a primitive teneurin by an ancestral

  8. Evolution of the MAGUK protein gene family in premetazoan lineages

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    Ruiz-Trillo Iñaki


    Full Text Available Abstract Background Cell-to-cell communication is a key process in multicellular organisms. In multicellular animals, scaffolding proteins belonging to the family of membrane-associated guanylate kinases (MAGUK are involved in the regulation and formation of cell junctions. These MAGUK proteins were believed to be exclusive to Metazoa. However, a MAGUK gene was recently identified in an EST survey of Capsaspora owczarzaki, an unicellular organism that branches off near the metazoan clade. To further investigate the evolutionary history of MAGUK, we have undertook a broader search for this gene family using available genomic sequences of different opisthokont taxa. Results Our survey and phylogenetic analyses show that MAGUK proteins are present not only in Metazoa, but also in the choanoflagellate Monosiga brevicollis and in the protist Capsaspora owczarzaki. However, MAGUKs are absent from fungi, amoebozoans or any other eukaryote. The repertoire of MAGUKs in Placozoa and eumetazoan taxa (Cnidaria + Bilateria is quite similar, except for one class that is missing in Trichoplax, while Porifera have a simpler MAGUK repertoire. However, Vertebrata have undergone several independent duplications and exhibit two exclusive MAGUK classes. Three different MAGUK types are found in both M. brevicollis and C. owczarzaki: DLG, MPP and MAGI. Furthermore, M. brevicollis has suffered a lineage-specific diversification. Conclusions The diversification of the MAGUK protein gene family occurred, most probably, prior to the divergence between Metazoa+choanoflagellates and the Capsaspora+Ministeria clade. A MAGI-like, a DLG-like, and a MPP-like ancestral genes were already present in the unicellular ancestor of Metazoa, and new gene members have been incorporated through metazoan evolution within two major periods, one before the sponge-eumetazoan split and another within the vertebrate lineage. Moreover, choanoflagellates have suffered an independent MAGUK

  9. Phylogenetic relationships of the intercellular fish pathogen Ichthyophonus hoferi and fungi, choanoflagellates and the rosette agent

    DEFF Research Database (Denmark)

    Spanggaard, Bettina; Skouboe, P.; Rossen, L.;


    Ichthyophonus hoferi Plehn and Mulsow, 1911 is thought to be one of the few pathogenic fungal infections of marine fish. The result of an attack is severe epizootics in herring stocks with drastic reduction in the population as a consequence. The exact phylogenetic position of the genus...... Ichthyophonus is not known. In the present study, a combination of molecular data, ultrastructure and biochemical characters were utilized to investigate the phylogeny of I. hoferi. The genomic DNA encoding the small subunit ribosomal RNA (18S rRNA) was amplified and sequenced. Comparisons with other eukaryotic...... 18S rRNA sequences indicate that I, hoferi is not a member of the Fungi. In both the parsimony and the neighbor-joining trees, I, hoferi is the sister taxon to the rosette agent. The clade encompassing I. hoferi and the rosette organism is the sister group to the choanoflagellate clade in the...

  10. Filter-feeding, near-field flows, and the morphologies of colonial choanoflagellates

    CERN Document Server

    Kirkegaard, Julius B


    Efficient uptake of nutrients from the environment is an important component in the fitness of all microorganisms, and its dependence on size may reveal clues to the origins of evolutionary transitions to multicellularity. Because potential benefits in uptake rates must be viewed in the context of other costs and benefits of size, such as varying predation rates and the increased metabolic costs associated with larger and more complex body plans, the uptake rate itself is not necessarily that which is optimized by evolution. Uptake rates can be strongly dependent on local organism geometry and its swimming speed, providing selective pressure for particular arrangements. Here we examine these issues for choanoflagellates, filter-feeding microorganisms that are the closest relatives of the animals. We explore the different morphological variations of the choanoflagellete $Salpingoeca~rosetta$, which can exist as a swimming cell, a sessile thecate cell, and as colonies of cells in various shapes. In the absence ...

  11. Early origin of the bilaterian developmental toolkit (United States)

    Erwin, Douglas H.


    Whole-genome sequences from the choanoflagellate Monosiga brevicollis, the placozoan Trichoplax adhaerens and the cnidarian Nematostella vectensis have confirmed results from comparative evolutionary developmental studies that much of the developmental toolkit once thought to be characteristic of bilaterians appeared much earlier in the evolution of animals. The diversity of transcription factors and signalling pathway genes in animals with a limited number of cell types and a restricted developmental repertoire is puzzling, particularly in light of claims that such highly conserved elements among bilaterians provide evidence of a morphologically complex protostome–deuterostome ancestor. Here, I explore the early origination of elements of what became the bilaterian toolkit, and suggest that placozoans and cnidarians represent a depauperate residue of a once more diverse assemblage of early animals, some of which may be represented in the Ediacaran fauna (c. 585–542 Myr ago). PMID:19571245

  12. Metazoan-like signaling in a unicellular receptor tyrosine kinase

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    Schultheiss Kira P


    Full Text Available Abstract Background Receptor tyrosine kinases (RTKs are crucial components of signal transduction systems in multicellular animals. Surprisingly, numerous RTKs have been identified in the genomes of unicellular choanoflagellates and other protists. Here, we report the first biochemical study of a unicellular RTK, namely RTKB2 from Monosiga brevicollis. Results We cloned, expressed, and purified the RTKB2 kinase, and showed that it is enzymatically active. The activity of RTKB2 is controlled by autophosphorylation, as in metazoan RTKs. RTKB2 possesses six copies of a unique domain (designated RM2 in its C-terminal tail. An isolated RM2 domain (or a synthetic peptide derived from the RM2 sequence served as a substrate for RTKB2 kinase. When phosphorylated, the RM2 domain bound to the Src homology 2 domain of MbSrc1 from M. brevicollis. NMR structural studies of the RM2 domain indicated that it is disordered in solution. Conclusions Our results are consistent with a model in which RTKB2 activation stimulates receptor autophosphorylation within the RM2 domains. This leads to recruitment of Src-like kinases (and potentially other M. brevicollis proteins and further phosphorylation, which may serve to increase or dampen downstream signals. Thus, crucial features of signal transduction circuitry were established prior to the evolution of metazoans from their unicellular ancestors.

  13. Preferential feeding and occupation of sunlit leaves favors defense response and development in the flea beetle, Altica brevicollis coryletorum--a pest of Corylus avellana. (United States)

    Łukowski, Adrian; Giertych, Marian J; Zadworny, Marcin; Mucha, Joanna; Karolewski, Piotr


    The monophagous beetle, Altica brevicollis coryletorum, is a major leaf pest of Corylus avellana (common hazel). In contrast to majority of the other studied species of shrubs, sunlit leaves are grazed to a much greater extent than shaded leaves. Since the observation of a link between leaf irradiance level and A. brevicollis feeding is unique, we hypothesized that feeding preference of this beetle species is related to the speed needed to escape threats i.e. faster jumping. We also hypothesized that sunlit leaves are more nutritious and easier to consume than the leaves of shaded shrubs. Results indicated that beetle mass was greater in beetles occupying sunlit leaves, which is consistent with our second hypothesis. The study also confirmed under laboratory conditions, that larvae, pupae and beetles that were fed full-light (100% of full light) leaves were significantly heavier than those fed with shaded leaves (15% of full light). In the high irradiance conditions (higher temperature) duration of larval development is also reduced. Further results indicated that neither the concentration of soluble phenols, leaf toughness, or the number of trichomes could explain the insect's preference for sunlit leaves. Notably, measurements of jump length of beetles of this species, both in the field and under laboratory conditions, indicated that the defense pattern related to jumping was associated with light conditions. The jump length of beetles in the sun was significantly higher than in the shade. Additionally, in laboratory tests, beetle defense (jumping) was more strongly affected by temperature (15, 25, or 35°C for 24 h) than by leaf type. The effect of sunlit, higher nutrient leaves (greater level of non-structural carbohydrates) on defense (jumping) appears to be indirect, having a positive effect on insect mass in all developmental stages. PMID:25927706

  14. New records of marine choanoflagellates off the Chilean coast Nuevos registros de coanoflagelados marinos de la costa de Chile

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    Katia Soto-Liebe


    Full Text Available This is the first report of planktonic choanoflagellates from the Chilean coast, relating their abundance with that of bacteria and viruses. Surface water samples were taken off Antofagasta, Montemar, and Puerto Montt and samples from ballast tanks were also analyzed. The choanoflagellates were identified following morphological type descriptions. Viruses and bacteria were stained with SYBR Green and choanoflagellates, bacteria, and viruses were counted simultaneously using red autofluorescence for the former and green fluorescence for the latter two. Six species of Acanthoecidae were observed for the first time in Chilean waters: Calliacantha multispina (0.3-10³ L-1, Acanthocorbis apoda, Stepha-noeca diplocostata (2.0-10³ L-1, Crinolina isefiordensis, Parvicorbicula superpositus, and Pleurasiga minima (5.0-10³ L-1. The concentrations of bacteria (1.1-10(6-4.5-10 6 and viral-like particles (VLPs (7.9-10 6-21-10(6 agreed with those typically found in marine coastal waters. In addition, Acanthocorbis asymmetrica was found in ballast waters, where its high concentration (20-10³ L-1 likely resulted from the particular physical and biological environment thereinEste es el primer reporte sobre coanoflagelados planctónicos de la costa chilena y su abundancia se relacionó con la de bacterias y virus. Se analizaron muestras de aguas superficiales obtenidas en Antofagasta, Montemar y Puerto Montt. Además se analizaron muestras adicionales de aguas provenientes de estanques de lastre. Los coanoflagelados se determinaron de acuerdo a descripciones morfológicas tipo. Virus y bacterias fueron teñidos con SYBR Green y la enumeración simultánea de coanoflagelados, bacterias y virus se determinó a través de autofluorescencia roja y fluorescencia verde respectivamente. Seis especies de Acanthoecidae fueron observadas por primera vez en aguas chilenas: Calliacantha multispina (0,3-10³ L-1, Acanthocorbis apoda y Stephanoeca diplocostata (2,0-10³ L

  15. Phylogeny of Tec family kinases identification of a premetazoan origin of Btk, Bmx, Itk, Tec, Txk, and the Btk regulator SH3BP5. (United States)

    Ortutay, Csaba; Nore, Beston F; Vihinen, Mauno; Smith, C I Edvard


    It is generally considered mammals and birds have five Tec family kinases (TFKs): Btk, Bmx (also known as Etk), Itk, Tec, and Txk (also known as Rlk). Here, we discuss the domains and their functions and regulation in TFKs. Over the last few years, a large number of genomes from various phyla have been sequenced making it possible to study evolutionary relationships at the molecular and sequence level. Using bioinformatics tools, we for the first time demonstrate that a TFK ancestor exists in the unicellular choanoflagellate Monosiga brevicollis, which is the closest known relative to metazoans with a sequenced genome. The analysis of the genomes for sponges, insects, hagfish, and frogs suggests that these species encode a single TFK. The insect form has a divergent and unique N-terminal region. Duplications generating the five members took place prior to the emergence of vertebrates. Fishes have two or three forms and the platypus, Ornithorhynchus anatinus, has four (lacks Txk). Thus, not all mammals have all five TFKs. The single identified TFK in frogs is an ortholog of Tec. Bmx seems to be unique to mammals and birds. SH3BP5 is a negative regulator of Btk. It is conserved in choanoflagellates and interestingly exists also in nematodes, which do not express TFKs, suggesting a broader function in addition to Btk regulation. The related SH3BP5-like protein is not found in Nematodes. PMID:19161832

  16. Nitrile hydratase genes are present in multiple eukaryotic supergroups.

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    Alan O Marron

    Full Text Available BACKGROUND: Nitrile hydratases are enzymes involved in the conversion of nitrile-containing compounds into ammonia and organic acids. Although they are widespread in prokaryotes, nitrile hydratases have only been reported in two eukaryotes: the choanoflagellate Monosiga brevicollis and the stramenopile Aureococcus anophagefferens. The nitrile hydratase gene in M. brevicollis was believed to have arisen by lateral gene transfer from a prokaryote, and is a fusion of beta and alpha nitrile hydratase subunits. Only the alpha subunit has been reported in A. anophagefferens. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the detection of nitrile hydratase genes in five eukaryotic supergroups: opisthokonts, amoebozoa, archaeplastids, CCTH and SAR. Beta-alpha subunit fusion genes are found in the choanoflagellates, ichthyosporeans, apusozoans, haptophytes, rhizarians and stramenopiles, and potentially also in the amoebozoans. An individual alpha subunit is found in a dinoflagellate and an individual beta subunit is found in a haptophyte. Phylogenetic analyses recover a clade of eukaryotic-type nitrile hydratases in the Opisthokonta, Amoebozoa, SAR and CCTH; this is supported by analyses of introns and gene architecture. Two nitrile hydratase sequences from an animal and a plant resolve in the prokaryotic nitrile hydratase clade. CONCLUSIONS/SIGNIFICANCE: The evidence presented here demonstrates that nitrile hydratase genes are present in multiple eukaryotic supergroups, suggesting that a subunit fusion gene was present in the last common ancestor of all eukaryotes. The absence of nitrile hydratase from several sequenced species indicates that subunits were lost in multiple eukaryotic taxa. The presence of nitrile hydratases in many other eukaryotic groups is unresolved due to insufficient data and taxon sampling. The retention and expression of the gene in distantly related eukaryotic species suggests that it plays an important metabolic role. The novel

  17. U12 type introns were lost at multiple occasions during evolution

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    Bartschat Sebastian


    Full Text Available Abstract Background Two categories of introns are known, a common U2 type and a rare U12 type. These two types of introns are removed by distinct spliceosomes. The phylogenetic distribution of spliceosomal RNAs that are characteristic of the U12 spliceosome, i.e. the U11, U12, U4atac and U6atac RNAs, suggest that U12 spliceosomes were lost in many phylogenetic groups. We have now examined the distribution of U2 and U12 introns in many of these groups. Results U2 and U12 introns were predicted by making use of available EST and genomic sequences. The results show that in species or branches where U12 spliceosomal components are missing, also U12 type of introns are lacking. Examples are the choanoflagellate Monosiga brevicollis, Entamoeba histolytica, green algae, diatoms, and the fungal lineage Basidiomycota. Furthermore, whereas U12 splicing does not occur in Caenorhabditis elegans, U12 introns as well as U12 snRNAs are present in Trichinella spiralis, which is deeply branching in the nematode tree. A comparison of homologous genes in T. spiralis and C. elegans revealed different mechanisms whereby U12 introns were lost. Conclusions The phylogenetic distribution of U12 introns and spliceosomal RNAs give further support to an early origin of U12 dependent splicing. In addition, this distribution identifies a large number of instances during eukaryotic evolution where such splicing was lost.

  18. The evolutionary diversification of LSF and Grainyhead transcription factors preceded the radiation of basal animal lineages

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    Kaufman Les


    Full Text Available Abstract Background The transcription factors of the LSF/Grainyhead (GRH family are characterized by the possession of a distinctive DNA-binding domain that bears no clear relationship to other known DNA-binding domains, with the possible exception of the p53 core domain. In triploblastic animals, the LSF and GRH subfamilies have diverged extensively with respect to their biological roles, general expression patterns, and mechanism of DNA binding. For example, Grainyhead (GRH homologs are expressed primarily in the epidermis, and they appear to play an ancient role in maintaining the epidermal barrier. By contrast, LSF homologs are more widely expressed, and they regulate general cellular functions such as cell cycle progression and survival in addition to cell-lineage specific gene expression. Results To illuminate the early evolution of this family and reconstruct the functional divergence of LSF and GRH, we compared homologs from 18 phylogenetically diverse taxa, including four basal animals (Nematostella vectensis, Vallicula multiformis, Trichoplax adhaerens, and Amphimedon queenslandica, a choanoflagellate (Monosiga brevicollis and several fungi. Phylogenetic and bioinformatic analyses of these sequences indicate that (1 the LSF/GRH gene family originated prior to the animal-fungal divergence, and (2 the functional diversification of the LSF and GRH subfamilies occurred prior to the divergence between sponges and eumetazoans. Aspects of the domain architecture of LSF/GRH proteins are well conserved between fungi, choanoflagellates, and metazoans, though within the Metazoa, the LSF and GRH families are clearly distinct. We failed to identify a convincing LSF/GRH homolog in the sequenced genomes of the algae Volvox carteri and Chlamydomonas reinhardtii or the amoebozoan Dictyostelium purpureum. Interestingly, the ancestral GRH locus has become split into two separate loci in the sea anemone Nematostella, with one locus encoding a DNA binding

  19. Flagellar apparatus structure of choanoflagellates. (United States)

    Karpov, Sergey A


    Phylum choanoflagellata is the nearest unicellular neighbor of metazoa at the phylogenetic tree. They are single celled or form the colonies, can be presented by naked cells or live in theca or lorica, but in all cases they have a flagellum surrounded by microvilli of the collar. They have rather uniform and peculiar flagellar apparatus structure with flagellar basal body (FB) producing a flagellum, and non-flagellar basal body (NFB) lying orthogonal to the FB. Long flagellar transition zone contains a unique structure among eukaryotes, the central filament, which connects central microtubules to the transversal plate. Both basal bodies are composed of triplets and interconnected with fibrillar bridge. They also contain the internal arc-shaped connectives between the triplets. The FB has prominent transitional fibers similar to those of chytrid zoospores and choanocytes of sponges, and a radial microtubular root system. The ring-shaped microtubule organizing center (MTOC) produces radial root microtubules, but in some species a MTOC is represented by separate foci. The NFB has a narrow fibrillar root directed towards the Golgi apparatus in association with membrane-bounded sac. Prior to cell division, the basal bodies replicate and migrate to poles of elongated nucleus. The basal bodies serve as MTOCs for the spindle microtubules during nuclear division by semiopen orthomitosis. PMID:27148446

  20. Thousands of rab GTPases for the cell biologist.

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    Yoan Diekmann


    Full Text Available Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate Monosiga brevicollis Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale

  1. Dicty_cDB: CHL545 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 1( DQ357217 |pid:none) Leishmania braziliensis elongation... 241 1e-62 AM494972_2...6( AM494972 |pid:none) Leishmania braziliensis chromosom... 241 1e-62 AY026074_1( AY026074 |pid:none) Monosiga brevicolli...eckkskvqng*fhnrsnschygps*kyq*yvcycscrsr*nhfirffnpkswyycr*s fw*yeiyvmsc**trxwyhh*ifiritslrnakgrqitswlyftri...fnqsyrfprsr*fq frsnccppcy*wcfxryrlrrkclrtnrncitssrr*tyqtslirqqsrsflirtpikh* rslslfp*sy*ir...... 241 1e-62 CT005272_19( CT005272 |pid:none) Leishmania major strain Friedlin,.

  2. Molecular evolution of Phox-related regulatory subunits for NADPH oxidase enzymes

    Directory of Open Access Journals (Sweden)

    Lambeth J David


    Full Text Available Abstract Background The reactive oxygen-generating NADPH oxidases (Noxes function in a variety of biological roles, and can be broadly classified into those that are regulated by subunit interactions and those that are regulated by calcium. The prototypical subunit-regulated Nox, Nox2, is the membrane-associated catalytic subunit of the phagocyte NADPH-oxidase. Nox2 forms a heterodimer with the integral membrane protein, p22phox, and this heterodimer binds to the regulatory subunits p47phox, p67phox, p40phox and the small GTPase Rac, triggering superoxide generation. Nox-organizer protein 1 (NOXO1 and Nox-activator 1 (NOXA1, respective homologs of p47phox and p67phox, together with p22phox and Rac, activate Nox1, a non-phagocytic homolog of Nox2. NOXO1 and p22phox also regulate Nox3, whereas Nox4 requires only p22phox. In this study, we have assembled and analyzed amino acid sequences of Nox regulatory subunit orthologs from vertebrates, a urochordate, an echinoderm, a mollusc, a cnidarian, a choanoflagellate, fungi and a slime mold amoeba to investigate the evolutionary history of these subunits. Results Ancestral p47phox, p67phox, and p22phox genes are broadly seen in the metazoa, except for the ecdysozoans. The choanoflagellate Monosiga brevicollis, the unicellular organism that is the closest relatives of multicellular animals, encodes early prototypes of p22phox, p47phox as well as the earliest known Nox2-like ancestor of the Nox1-3 subfamily. p67phox- and p47phox-like genes are seen in the sea urchin Strongylocentrotus purpuratus and the limpet Lottia gigantea that also possess Nox2-like co-orthologs of vertebrate Nox1-3. Duplication of primordial p47phox and p67phox genes occurred in vertebrates, with the duplicated branches evolving into NOXO1 and NOXA1. Analysis of characteristic domains of regulatory subunits suggests a novel view of the evolution of Nox: in fish, p40phox participated in regulating both Nox1 and Nox2, but after the

  3. Dicty_cDB: Contig-U15846-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available clone KBrB086B23,... 38 0.42 10 ( AF538053 ) Monosiga brevicollis mitochondrion, complet...mal pr... 48 1.2 1 ( AY630685 ) Symplocos brenesii isolate Rsbrenesii424 ribosoma... 48 1.2 1 ( AY630684 ) Symplocos... breedlovei isolate RSbreedlovei431 ribo... 48 1.2 1 ( AY630683 ) Symplocos...lichotricha10... 48 1.2 1 ( AY630705 ) Symplocos austrosinensis isolate RSaustrosinensis...2 1 ( AY336391 ) Symplocos domingensis isolate RSdomingensisA5202 ... 48 1.2 1 ( AY336390 ) Symplocos

  4. Dicty_cDB: Contig-U00742-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available A... 38 2.3 9 ( AF538053 ) Monosiga brevicollis mitochondrion, complete genome. 4...mal RNA ge... 34 0.43 4 ( AC117081 ) Dictyostelium discoideum chromosome 2 map 5862124... 38 0.43 15 ( BD453072 ) Diagnosis of Dis...8 0.82 6 ( CP000678 ) Methanobrevibacter smithii ATCC 35061, complete g... 36 0.83 18 ( AM426422 ) Vitis vin...0 6 ( EU002242 ) Melianthus comosus NADH-plastoquinone oxidoreduct... 42 4.0 3 ( AC093296 ) Homo sapiens chromoso...coideum chromosome 2 map 5201047... 36 0.008 16 ( EU677193 ) Oedo

  5. AcEST: BP917446 [AcEST

    Lifescience Database Archive (English)

    Full Text Available OS=Debaryomyces hanse... 94 3e-19 sp|Q4ICA8|RUVB1_GIBZE RuvB-like helicase 1 OS=Gibberella zeae GN... 92 1e...ntin OS=Volvox carteri f. nagariensis G... 122 9e-27 tr|Q9M3Z6|Q9M3Z6_CICAR Putative Ruv DNA-helicase OS=Cic... OS=Monosiga brevicollis... 109 8e-23 tr|Q5ZIC4|Q5ZIC4_CHICK Putative uncharacterized protein OS=Gallu... 10...ALLL GAPGTGK Sbjct: 61 MAGRALLLTGAPGTGK 76 >tr|Q9M3Z6|Q9M3Z6_CICAR Putative Ruv mRNA. clone: YMU001_000100_H09. Accession BP917446 Tissue type prothallium Developmental stage - Contig ID - Sequence GTCTTGCCA

  6. AcEST: BP913692 [AcEST

    Lifescience Database Archive (English)

    Full Text Available BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= BP913692|Adia...tion of protein database search programs, Nucleic Acids Res. 25:3389-3402. Query= BP913692|Adiantum capillus-vener...ntum capillus-veneris mRNA, clone: YMU001_000033_B12. (601 letters) Database: uniprot_tr...mosome undetermined scaffold_334, who... 84 6e-15 tr|B2ZTQ6|B2ZTQ6_SEPES Muscle myosin heavy chain OS=Sepia escule...9V6R9|A9V6R9_MONBE Predicted protein OS=Monosiga brevicollis... 45 0.003 tr|B2ZTQ5|B2ZTQ5_LOLBL Muscle myosi

  7. Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans

    Directory of Open Access Journals (Sweden)

    Chen Nansheng


    Full Text Available Abstract Background Intraflagellar transport (IFT genes, which are critical for the development and function of cilia and flagella in metazoans, are tightly regulated by the Regulatory Factor X (RFX transcription factors (TFs. However, how and when their evolutionary relationship was established remains unknown. Results We have identified evidence suggesting that RFX TFs and IFT genes evolved independently and their evolution converged before the first appearance of metazoans. Both ciliary genes and RFX TFs exist in all metazoans as well as some unicellular eukaryotes. However, while RFX TFs and IFT genes are found simultaneously in all sequenced metazoan genomes, RFX TFs do not co-exist with IFT genes in most pre-metazoans and thus do not regulate them in these organisms. For example, neither the budding yeast nor the fission yeast possesses cilia although both have well-defined RFX TFs. Conversely, most unicellular eukaryotes, including the green alga Chlamydomonas reinhardtii, have typical cilia and well conserved IFT genes but lack RFX TFs. Outside of metazoans, RFX TFs and IFT genes co-exist only in choanoflagellates including M. brevicollis, and only one fungus Allomyces macrogynus of the 51 sequenced fungus genomes. M. brevicollis has two putative RFX genes and a full complement of ciliary genes. Conclusions The evolution of RFX TFs and IFT genes were independent in pre-metazoans. We propose that their convergence in evolution, or the acquired transcriptional regulation of IFT genes by RFX TFs, played a pivotal role in the establishment of metazoan.

  8. Role of diatom-attached choanoflagellates of the genus Salpingoeca as pelagic bacterivores

    Czech Academy of Sciences Publication Activity Database

    Šimek, Karel; Jezbera, Jan; Horňák, Karel; Vrba, Jaroslav; Seďa, Jaromír


    Roč. 36, č. 3 (2004), s. 257-269. ISSN 0948-3055 R&D Projects: GA ČR(CZ) GA206/02/0003 Keywords : reservoir * microbial food webs * protistan bacterivory Subject RIV: EE - Microbiology, Virology Impact factor: 2.255, year: 2004

  9. Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom

    Directory of Open Access Journals (Sweden)

    Heitman Joseph


    Full Text Available Abstract Background The nutrient-sensing Tor pathway governs cell growth and is conserved in nearly all eukaryotic organisms from unicellular yeasts to multicellular organisms, including humans. Tor is the target of the immunosuppressive drug rapamycin, which in complex with the prolyl isomerase FKBP12 inhibits Tor functions. Rapamycin is a gold standard drug for organ transplant recipients that was approved by the FDA in 1999 and is finding additional clinical indications as a chemotherapeutic and antiproliferative agent. Capitalizing on the plethora of recently sequenced genomes we have conducted comparative genomic studies to annotate the Tor pathway throughout the fungal kingdom and related unicellular opisthokonts, including Monosiga brevicollis, Salpingoeca rosetta, and Capsaspora owczarzaki. Results Interestingly, the Tor signaling cascade is absent in three microsporidian species with available genome sequences, the only known instance of a eukaryotic group lacking this conserved pathway. The microsporidia are obligate intracellular pathogens with highly reduced genomes, and we hypothesize that they lost the Tor pathway as they adapted and streamlined their genomes for intracellular growth in a nutrient-rich environment. Two TOR paralogs are present in several fungal species as a result of either a whole genome duplication or independent gene/segmental duplication events. One such event was identified in the amphibian pathogen Batrachochytrium dendrobatidis, a chytrid responsible for worldwide global amphibian declines and extinctions. Conclusions The repeated independent duplications of the TOR gene in the fungal kingdom might reflect selective pressure acting upon this kinase that populates two proteinaceous complexes with different cellular roles. These comparative genomic analyses illustrate the evolutionary trajectory of a central nutrient-sensing cascade that enables diverse eukaryotic organisms to respond to their natural

  10. Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes (United States)

    Holden, Todd; Dehipawala, S.; Cheung, E.; Bienaime, R.; Ye, J.; Tremberger, G., Jr.; Schneider, P.; Lieberman, D.; Cheung, T.


    The Rubisco protein-enzyme is arguably the most abundance protein on Earth. The biology dogma of transcription and translation necessitates the study of the Rubisco genes and Rubisco-like genes in various species. Stronger correlation of fractal dimension of the atomic number fluctuation along a DNA sequence with Shannon entropy has been observed in the studied Rubisco-like gene sequences, suggesting a more diverse evolutionary pressure and constraints in the Rubisco sequences. The strategy of using metal for structural stabilization appears to be an ancient mechanism, with data from the porphobilinogen deaminase gene in Capsaspora owczarzaki and Monosiga brevicollis. Using the chi-square distance probability, our analysis supports the conjecture that the more ancient Rubisco-like sequence in Microcystis aeruginosa would have experienced very different evolutionary pressure and bio-chemical constraint as compared to Bordetella bronchiseptica, the two microbes occupying either end of the correlation graph. Our exploratory study would indicate that high fractal dimension Rubisco sequence would support high carbon dioxide rate via the Michaelis- Menten coefficient; with implication for the control of the whooping cough pathogen Bordetella bronchiseptica, a microbe containing a high fractal dimension Rubisco-like sequence (2.07). Using the internal comparison of chi-square distance probability for 16S rRNA (~ E-22) versus radiation repair Rec-A gene (~ E-05) in high GC content Deinococcus radiodurans, our analysis supports the conjecture that high GC content microbes containing Rubisco-like sequence are likely to include an extra-terrestrial origin, relative to Deinococcus radiodurans. Similar photosynthesis process that could utilize host star radiation would not compete with radiation resistant process from the biology dogma perspective in environments such as Mars and exoplanets.

  11. New insights on the sialidase protein family revealed by a phylogenetic analysis in metazoa.

    Directory of Open Access Journals (Sweden)

    Edoardo Giacopuzzi

    Full Text Available Sialidases are glycohydrolytic enzymes present from virus to mammals that remove sialic acid from oligosaccharide chains. Four different sialidase forms are known in vertebrates: the lysosomal NEU1, the cytosolic NEU2 and the membrane-associated NEU3 and NEU4. These enzymes modulate the cell sialic acid content and are involved in several cellular processes and pathological conditions. Molecular defects in NEU1 are responsible for sialidosis, an inherited disease characterized by lysosomal storage disorder and neurodegeneration. The studies on the biology of sialic acids and sialyltransferases, the anabolic counterparts of sialidases, have revealed a complex picture with more than 50 sialic acid variants selectively present in the different branches of the tree of life. The gain/loss of specific sialoconjugates have been proposed as key events in the evolution of deuterostomes and Homo sapiens, as well as in the host-pathogen interactions. To date, less attention has been paid to the evolution of sialidases. Thus we have conducted a survey on the state of the sialidase family in metazoan. Using an in silico approach, we identified and characterized sialidase orthologs from 21 different organisms distributed among the evolutionary tree: Metazoa relative (Monosiga brevicollis, early Deuterostomia, precursor of Chordata and Vertebrata (teleost fishes, amphibians, reptiles, avians and early and recent mammals. We were able to reconstruct the evolution of the sialidase protein family from the ancestral sialidase NEU1 and identify a new form of the enzyme, NEU5, representing an intermediate step in the evolution leading to the modern NEU3, NEU4 and NEU2. Our study provides new insights on the mechanisms that shaped the substrate specificity and other peculiar properties of the modern mammalian sialidases. Moreover, we further confirm findings on the catalytic residues and identified enzyme loop portions that behave as rapidly diverging regions and may

  12. A Tale of Two Drug Targets: The Evolutionary History of BACE1 and BACE2

    Directory of Open Access Journals (Sweden)

    Christopher eSouthan


    Full Text Available The beta amyloid (APP cleaving enzyme (BACE1 has been a drug target for Alzheimer's Disease (AD since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralogue, BACE2, became a new target for type II diabetes (T2DM having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologues (UrBACEs in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans. UrBACEs are predominantly single copy, show 35% to 45% protein sequence identity with mammalian BACE1, are approximately 100 residues longer than cathepsin paralogues with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogues in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5’ exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.

  13. Aerotaxis in the Closest Relatives of Animals

    CERN Document Server

    Kirkegaard, Julius B; Marron, Alan O; Leptos, Kyriacos C; Goldstein, Raymond E


    As the closest unicellular relatives of animals, choanoflagellates serve as useful model organisms for understanding the evolution of animal multicellularity. An important factor in animal evolution was the increasing ocean oxygen levels in the Precambrian, which are thought to have influenced the emergence of complex multicellular life. As a first step in addressing these conditions, we study here the response of the colony-forming choanoflagellate $Salpingoeca~rosetta$ to oxygen gradients. Using a microfluidic device that allows spatio-temporal variations in oxygen concentrations, we report the discovery that $S.~rosetta$ display positive aerotaxis. Analysis of the spatial population distributions provides evidence for logarithmic sensing of oxygen, which enhances sensing in low oxygen neighborhoods. Analysis of search strategy models on the experimental colony trajectories finds that choanoflagellate aerotaxis is consistent with stochastic navigation, the statistics of which are captured using an effective...

  14. Dicty_cDB: Contig-U13335-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s... 46 2.8 1 ( AY583768 ) Antirhea borbonica clone AntbT10B microsatellite ... 46 2.8 1 ( AC004557 ) Genomic sequen...2 1 ( AP008217 ) Oryza sativa (japonica cultivar-group) genomic DN... 48 0.72 1 ( AC147812 ) Oryza sativa Japonica Group chromos...2 1 ( AP008158 ) Lotus japonicus genomic DNA, chromosome 3, clone:... 48 0.72 1 ( AC176106 ) 48 0.72 1 ( DH499839 ) Monosiga ovata DNA, fosmid clone: MOF-067C09, gen...... 48 0.72 1 ( DH493979 ) Monosiga ovata DNA, fosmid clone: MOF-056L19, gen... 48 0.72 1 ( CG946880 ) MBEDE22T

  15. Evolutionary relationships of Metazoa within the eukaryotes based on molecular data from Porifera.


    Schütze, J; Krasko, A.; Custodio, M R; Efremova, S M; Müller, I M; Müller, W E


    Recent molecular data provide strong support for the view that all metazoan phyla, including Porifera, are of monophyletic origin. The relationship of Metazoa, including the Porifera, to Plantae, Fungi and unicellular eukaryotes has only rarely been studied by using cDNAs coding for proteins. Sequence data from rDNA suggested a relationship of Porifera to unicellular eukaryotes (choanoflagellates). However, ultrastructural studies of choanocytes did not support these findings. In the present ...

  16. Cadherin evolution and the origin of animals


    Abedin, Monika


    The question of how animals evolved from a unicellular ancestor has challenged evolutionary biologists for decades. Because cell adhesion and signaling are required for multicellularity, understanding how these cellular processes evolved will provide key insights into the origin of animals. A critical finding is that choanoflagellates, the closest living unicellular relatives of animals, express members of the cadherin superfamily. Cadherins are pivotal for animal cell adhesion and signali...

  17. Adaptive evolution of voltage-gated sodium channels: The first 800 million years


    Zakon, Harold H.


    Voltage-gated Na+-permeable (Nav) channels form the basis for electrical excitability in animals. Nav channels evolved from Ca2+ channels and were present in the common ancestor of choanoflagellates and animals, although this channel was likely permeable to both Na+ and Ca2+. Thus, like many other neuronal channels and receptors, Nav channels predated neurons. Invertebrates possess two Nav channels (Nav1 and Nav2), whereas vertebrate Nav channels are of the Nav1 family. Approximately 500 Mya ...

  18. AcEST: DK954316 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST39A01NGRL0020_B23 601 Adiantum capillus-veneris mRNA. clone: TST39A01NGRL0020_B23. 5' end seq ... cha... 69 2e-11 sp|Q9VHT4|FUCT1_DROME Probable GDP-fucose ... transporter OS=Drosoph... 59 2e-08 sp|P39542|YJT3_ ... ucose/GDP-ma... 42 0.003 sp|A9UUB8|FUCT1_MONBE GDP-fucose ... transporter 1 OS=Monosiga brevi... 40 0.007 sp|P22 ...

  19. Dicty_cDB: Contig-U15561-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Y392443 ) Dictyostelium discoideum possible endotoxin gene,... 38 0.43 3 ( AB253466 ) Chlamy...3 ( DH480527 ) Monosiga ovata DNA, fosmid clone: MOF-033G07, gen... 40 0.001 4 ( EX845925 ) CBNC6139.fwd CBNC blakesleeanus NRRL15... 54 0.002 2 ( EX850982 ) CBNC8772.fwd CBNC Phycomyces blakesleeanus NRRL...cDN... 54 0.031 1 ( EX850403 ) CBNC8454.fwd CBNC Phycomyces blakesleeanus NRRL15... 54 0.031 1 ( BH059078 ) ...Picea... 52 0.12 1 ( EF686414 ) Kirramyces destructans strain CMW19921 microsatel... 42 0.13 2 ( EF686413 ) Kirramyces destructans

  20. AcEST: BP918568 [AcEST

    Lifescience Database Archive (English)

    Full Text Available YMU001_000115_A08 561 Adiantum capillus-veneris mRNA. clone: YMU001_000115_A08. BP918568 CL2767C ... e incorporator OS=Monosiga b... 74 5e-13 sp|Q12116|TMS 1_YEAST Membrane protein TMS 1 OS=Saccharomyces cere ... haliana PE=2 SV=1 206 7e-52 tr|Q10IH0|Q10IH0_ORYSJ TMS ... membrane family protein, putative, ex... 206 7e-52 ...

  1. Dicty_cDB: Contig-U08227-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available letters Score E Sequences producing significant alignments: (bits) Value Contig-U08227-1 (Contig-U08227-1Q) /CSM_Contig/Cont...osiga brevicollis mitochondrion, complete genome. 36 0.009 8 ( AF250284 ) Amsacta moorei ent...e Score E Sequences producing significant alignments: (bits) Value AY392438_1( AY392438 |pid:none) Dictyosteli...e Score E Sequences producing significant alignments: (bits) Value N ( AY392443 ) Dictyostelium discoideum possible en...ce 3 from Patent WO03072812. 36 0.11 7 ( AE014848 ) Plasmodium falciparum 3D7 chromosome 12, section

  2. Influence of polychlorinated biphenyls on the growth of chicken embryos

    Energy Technology Data Exchange (ETDEWEB)

    Hatano, Yasuhiko; Hatano, Akira [Chub Women`s College, Gifu-ken (Japan)


    Incubation of chicken embryos with either 0.01 or 0.03 ppm polychlorinated biphenyls (PCBs) for 12, 15, or 18 d resulted in a significant decrease in liver and body weight associated with enhanced mortality. Teratological examination revealed an increased frequency of malformations including hydrops, eventration, wry neck, and brevicollis. PCB exposure was also found to produce histologic damage to liver and cutaneous tissue. Our data demonstrate that exposure of chicks to PCBs during development results in a retardation of growth, an increased incidence of malformations, and histopathologic damage. 9 refs., 2 figs., 4 tabs.

  3. AcEST: DK952626 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST38A01NGRL0014_J18 551 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0014_J18. 5' end seq ... osiga brevicollis... 34 5.9 tr|Q99NK1|Q99NK1_HYDHY Tyrosinase ... (Fragment) OS=Hydrochoerus hyd... 33 7.7 tr|B5H7A0 ... protein OS=Strep... 33 7.7 tr|A6MN58|A6MN58_EPTFU Tyrosinase ... (Fragment) OS=Eptesicus fuscus... 33 7.7 tr|Q5G686 ...

  4. Morphology and distribution of heterotrophic protists along 75゜E in the Southern Ocean




    Seawater samples were collected from the 0 and 50m layers along the transect of 75°E in the Indian sector of the Southern Ocean in the austral summer of 1983-84 during the BIOMASS SIBEX I cruise of the R. V. KAIYO MARU of Japan Fisheries Agency. Distribution and taxonomy of heterotrophic protists were investigated. Naked amoebae and choanoflagellates were the dominant heterotrophic protists in the Indian sector of the Southern Ocean. The total cell volume of heterotrophic protists was larger ...

  5. Dicty_cDB: Contig-U03720-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available nlylyhhhyl nv*v*kfedtfheli*lqvnvnl*sth*l*i**sflllkf*dynyyyyhhhhy*idlkvi liilk*nplgqf*i Frame C: fffllvnlnfiyfyfcfyfyfyfyfylifffffs...yf*yynlknipihifit*kiiflfff ffffffffflrin*nifkkpinfiifpriilfsiftwfliidiweniihkk*ei*sf*nc w*ynfk*lif...I-EH-IJ0 Emiliania hu... 52 0.032 1 ( CV022859 ) Rasgscb0446 Salivary Gland 4th instar 3rd period ... 52 0.0...32 1 ( CK813625 ) Rasgsc3435 Salivary Gland 4th instar 3rd period (... 52 0.032 1 ( CK811885 ) Rasgsc7951 Salivary Gland 4th instar...utum genomic ... 50 0.13 1 ( DU393607 ) 1098397073483 CHORI-243 Ovis aries genomic clone ... 50 0.13 1 ( DH492858 ) Monosiga ovata

  6. Dicty_cDB: Contig-U09164-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available quence (All Frames) Frame A: hps*n*lrnisnwkrd*kslvanynnpsrhrqwtnsnlgnwfslkisrkeltrnlansqt ...rti... 54 0.010 1 ( CR049178 ) Forward strand read from insert in 5'HPRT inserti... 54 0.010 1 >( BJ415009 ) Dictyostel...4 List of clone(s) est1= VFK306F ,1,609 est2= SLD323F ,198,508 est3= SLD323Z ,610,989 est4= VFK306Z ,644,895 Trans...CIYR FRVHGYRNSSSRTRTNTNYSRGTIF*trrd*sttn*tn*tn*tn*kttti**iinykrfw kiknkkik Translated Amino Acid se...genomic cl... 54 0.010 1 ( DH477779 ) Monosiga ovata DNA, fosmid clone: MOF-028J10, gen... 54 0.010 1 ( DE222678 ) Trifolium pratense

  7. Dicty_cDB: Contig-U12636-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ) Eutagenia smyrnensis partial mp20 ... 35 2.0 CU928178_255( CU928178 |pid:none) Zygosaccharomyces rouxii strain...s-contain... 47 5e-04 FM877202_1( FM877202 |pid:none) Eutagenia sp. AP3 partial mp20 gen...5 CR382128_171( CR382128 |pid:none) Yarrowia lipolytica strain CLIB1... 52 1e-05 AJ514262_1( AJ514262 |pid:none) Cicindela goon parti...) Monosiga ovata MoPTK-h mRNA for pr... 51 3e-05 AJ514284_1( AJ514284 |pid:none) Cicindela dysenterica partia...) Opatroides punctulatus partial mp2... 50 6e-05 BC143883_1( BC143883 |pid:none) Homo sapiens leucine

  8. Dicty_cDB: Contig-U15999-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available DQ120986 ) Hucho taimen clone ZB-41 microsatellite sequence. 42 0.38 2 ( FE260308 ) CAZN834.fwd CAZN Naegleria gruberi Flagellat... 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 cds. 40 0.025 2 ( EG551347 ) MM01C22_XP Sugar Beet germination cDNA library Be... 40 0.025 2 ( DH506983 ) Monosiga ovat...e MegEu13 microsatellite ... 40 1.9 2 ( BP024203 ) Ciona intestinalis cDNA, clon...ent US 7314974. 34 4.6 2 ( FE268718 ) CAZO773.fwd CAZO Naegleria gruberi Flagellate Sta... 40 4.6 2 ( DY

  9. Dicty_cDB: Contig-U01201-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available DT573931 ) EST1084571 GH_TMO Gossypium hirsutum cDNA, mRNA s... 46 2.3 1 ( DR026249 ) Osmo00116 F. cylindrus...114264 ) Homo sapiens clone HH409 unknown mRNA. 36 6.3 3 ( AZ544391 ) ENTEP49TR Entamoeba histolytica Sheare...Monosiga ovata DNA, fosmid clone: MOF-072C15, gen... 44 9.0 1 ( CG956333 ) MBEFK13TR mth2 Medicago truncatul...Acid Glyc... 44 9.0 1 ( CB895022 ) EST647814 HOGA Medicago truncatula cDNA clone HOG... 44 9.0 1 ( CB894878 ...) EST647670 HOGA Medicago truncatula cDNA clone HOG... 44 9.0 1 ( CB891192 ) EST648161 KV3 Medicago trun

  10. Dicty_cDB: AFJ515 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available -C/VSB355Q.Seq.d/ 34 0.83 own update 2002. 9.17 Homology vs DNA Score E Sequences producing significant alig...ult infected midgut library, clone Tse3b04_p1c. 30 5.9 2 AF538053 |AF538053.1 Monosiga brevicol...fx--- Frame C: k*if*ykkv*l*iiiiiifqlfkyfyniffffxat*nl*xesfxeyspxp*rxscfyxex vxqxrll*sf--- Homology vs CSM-cDNA Sco...s thaliana TDNA insertion lines Arabidopsis thaliana genomic clone SALK_006746.29.99.f, DN...92565. 32 8.5 2 dna update 2003. 9. 5 Homology vs Protein ***** No hits found ****** Lambda K H 0.318 0.134

  11. AcEST: BP913077 [AcEST

    Lifescience Database Archive (English)

    Full Text Available LLMEGIDDLSQEAYKFQQYHRNATKAKASLDAQLEARRAEN 286 >sp|A7SA47|EIF3H_NEMVE Eukaryotic translation initiation factor 3 subunit H OS=Nematos...NFSRLYLTKALHDN 337 >sp|A9V3P1|EIF3H_MONBE Eukaryotic translation initiation factor 3 subunit H OS=Monosiga b...QKHQYQQRRQQENM 286 >sp|Q56JZ5|EIF3H_BOVIN Eukaryotic translation initiation factor 3 subunit H OS=Bos...ion sp|Q9C5Z2|EIF3H_ARATH Eukaryotic translation initiation factor 3 subunit H OS=Arabidopsis thaliana ...ficant alignments: (bits) Value sp|Q9C5Z2|EIF3H_ARATH Eukaryotic translation initiation factor 3...

  12. Dicty_cDB: Contig-U15359-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 00450_519( CP000450 |pid:none) Nitrosomonas eutropha C91, compl... 60 3e-07 CP000300_1111( CP000300 |pid:none) Methanococco...1H2 sequ... 48 0.91 1 ( DQ191761 ) Monosiga ovata Hoglet (hoglet) mRNA, complete cds. 48 0.91 1 ( AY013583 ) Haliotis kamtschatkana...lyphosphate kinase (PP... 48 0.91 1 ( AE014298 ) Drosophila melanogaster chromosome X, comp...9 CP000713_1310( CP000713 |pid:none) Psychrobacter sp. PRwf-1, compl... 66 3e-09 CP000099_988( CP000099 |pid:none) Erwinia tasmaniensis strain ET1... 64 1e-08 CP000744_77( CP000744 |pid:none) Pseudomonas aeruginosa PA7, comp

  13. Dicty_cDB: Contig-U01558-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available *f*iqknntkk*ykk ntkki own update 2004. 6. 7 Homology vs CSM-cDNA Query= Contig-U01558-1 (Contig-U01558-1Q) /....9 bits) X2: 15 (29.7 bits) S1: 12 (24.3 bits) S2: 15 (30.2 bits) dna update 2009. 5. 1 Homolog..._Ba0210I23.r OC__Ba Oryza coarctata genomic cl... 40 0.027 2 ( DE226514 ) Trifolium pratense DNA, clone:RCG1...... 50 0.13 1 ( DH464435 ) Monosiga ovata DNA, fosmid clone: MOF-005B13, gen... 50 0.13 1 ( CR165209 ) Forward strand re...2 ) Nicotiana plumbaginifolia 120 kDa pistil extensin... 46 2.0 1 ( AP010372 ) Lotus japonicus genomic DNA, chromosome 1, clo

  14. AcEST: BP917058 [AcEST

    Lifescience Database Archive (English)

    Full Text Available eil... 35 1.9 tr|B1ZN10|B1ZN10_OPITP Phosphoribosylaminoimidazolecarboxamide f... 35 1.9 tr|Q4S5V2|Q4S5V2_TE...0_OPITP Phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase OS=Opitutus terrae (str...bergh... 32 1.6 sp|P23093|CSP_PLABA Circumsporozoite protein OS=Plasmodium bergh... 32 1.6 sp|Q52978|PHAAB_RHIME Probable...4G9K3|B4G9K3_DROPE GL18634 OS=Drosophila persimilis GN=GL186... 34 4.2 tr|A9V1P2|A9V1P2_MONBE Predicted protein OS=Monosiga brevicol...r|A0D5X1|A0D5X1_PARTE Chromosome undetermined scaffold_39, whole genome shotgun sequence OS=Paramecium tetra

  15. An annotated catalogue of the Iranian Euphorinae, Gnamptodontinae, Helconinae, Hormiinae and Rhysipolinae (Hymenoptera: Braconidae). (United States)

    Gadallah, Neveen S; Ghahari, Hassan; Achterberg, Kees Van


    The Iranian species diversity of five braconid subfamilies, Euphorinae (54 species in 16 genera and 8 tribes), Gnamptodontinae (4 species in 1 genus and 1 tribe), Helconinae (9 species in 5 genera and 2 tribes), Hormiinae (8 species in 4 genera and 2 tribe) and Rhysipolinae (3 species in 2 genera) are summarized in this catalogue. A faunistic list is given comprising both local and global distribution of each species under study as well as host records. In the present study ten new records are added to the Iranian fauna: Centistes (Ancylocentrus) ater (Nees), Centistes cuspidatus (Haliday), Meteorus affinis (Wesmael), Meteorus rufus (DeGeer), Microctonus brevicollis (Haliday), Microctonus falciger Ruthe, Peristenus nitidus (Curtis) (Euphorinae), Aspicolpus carinator (Nees), Diospilus capito (Nees) and Diospilus productus Marshall (Helconinae s.l.). Euphorus pseudomitis Hedwig, 1957 is transferred to the subfamily Hormiinae and Hormisca pseudomitis (Hedwig, 1957) is a new combination. PMID:27395908


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    Urquiza-Bardone, Sergio


    Full Text Available The emergence of multicellularity and epithelia in relation to the appearance of cellular junctions, in order to illustrate the first steps of animal evolution, is discussed. We analyzed the structure and roles of adherens and occludins, considered to be the oldest. Also treated are some aspects of the main proteins that constitute them, the cadherins and claudins, as well as the related structures observed in sponges and choanoflagellates, the most ancient animals and the ancestors of these, respectively. It was concluded that the animal ancestor probably possessed some kind of adherens and possibly occludins, appearing as the first of major importance. These junctions increased in complexity through until the complexity observed in modern times.

  17. A small short-necked hupehsuchian from the lower Triassic of Hubei Province, China.

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    Xiao-hong Chen

    Full Text Available Hupehsuchia is a group of enigmatic Triassic marine reptiles that is known exclusively from two counties in Hubei Province, China. One of the common features of the group was a modestly long neck with nine to ten cervical vertebrae. We report a new species of Hupehsuchia, Eohupehsuchus brevicollis gen. et sp. nov., which for the first time shows a short neck in this group, with six cervicals. The configuration of the skull roof in Eohupehsuchus is also unique among Hupehsuchia, with narrow frontals and posteriorly shifted parietals, warranting recognition of a new species. The taxon superficially resembles Nanchangosaurus in retaining hupehsuchian plesiomorphies, such as low neural spines and small body size. However, its limbs are well-developed, unlike in Nanchangosaurus, although the latter genus is marginally larger in body length. Thus, the individual is unlikely to be immature. Also, Eohupehsuchus shares a suite of synapomorphies with Hupehsuchus, including the second and third layers of dermal ossicles above the dorsal neural spines. A phylogenetic analysis suggests that the new species is not the most basal hupehsuchian despite its short neck, and instead forms the sister taxon of Hupehsuchidae. Until recently, Hupehsuchia contained only two monotypic genera. Now there are at least four genera among Hupehsuchia, and the undescribed diversity is even higher. The left forelimb of the only specimen is incomplete, ending with broken phalanges distally. The breakage could only have occurred pre-burial. The individual may have been attacked by a predator and escaped, given that scavenging is unlikely.

  18. The role of historical and ecological factors on initial survival of Copaifera langsdorffii Desf. (Fabaceae

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    Marcílio Fagundes


    Full Text Available The plant population dynamic is affected by ecological and evolutionary processes that operate at all stages of the plant life cycle. The aim of this study was to characterize the seed and seedling performance of Copaifera langsdorffii by testing four hypotheses: the resource concentration hypothesis; the relationship between seed size and germinability hypothesis; the relationship between seed size and seedling vigor hypothesis; and the intraspecific seedling competition hypothesis. All seeds used in the experiments were collected from 35 C. langsdorffii plants located in a fragment of the Brazilian cerrado (savanna. The number of fruits per plant negatively affected Rhinochenus brevicollis attacks on C. langsdorffii seeds. Therefore, this result does not support the resource concentration hypothesis, and predator satiation was used in order to explain the observed result. In general, seed germinability (percentage and time to emergence was not influenced by seed size. The homogeneity of the experimental design, together with an abundant water supply, may have masked the effects of seed size on germinability. Seed size positively affected seedling development, corroborating the expected relationship between seed size and seedling vigor. The number of seedling per plastic bags negatively affected the growth of C. langsdorffii. The nutrient-limited soil probably promoted the below-ground competition for nutrients among seedlings. Finally, the role of evolutionary and ecological factors on C. langsdorffii population dynamics is discussed.

  19. Season and light affect constitutive defenses of understory shrub species against folivorous insects (United States)

    Karolewski, Piotr; Giertych, Marian J.; Żmuda, Michał; Jagodziński, Andrzej M.; Oleksyn, Jacek


    Understory shrubs contribute to overall species diversity, providing habitat and forage for animals, influence soil chemistry and forest microclimate. However, very little is known about the chemical defense of various shrub species against folivorous insects. Using six shrub species, we tested how seasonal changes and light conditions affect their constitutive defense to insect damage. We monitored leaf perforation, concentrations of total phenols, condensed tannins, nitrogen (N), and total nonstructural carbohydrates (TNC). Leaf damage caused by insects was low in Sambucus nigra, Cornus sanguinea, and Frangula alnus, intermediate in Corylus avellana and Prunus serotina, and high in Prunus padus. Leaves of all the species, when growing in high light conditions, had high concentrations of defense metabolites. Except for C. avellana, leaves of the other shrub species growing in full sun were less injured than those in shade. This may be due to higher concentrations of defense metabolites and lower concentrations of nitrogen. Similar patterns of the effects of light on metabolites studied and N were observed for leaves with varying location within the crown of individual shrubs (from the top of the south direction to the bottom of the north), as for leaves from shrubs growing in full sun and shrubs in the shade of canopy trees. A probable cause of the greater damage of more sunlit leaves of C. avellana was the fact that they were herbivorized mostly by Altica brevicollis, a specialist insect that prefers plant tissues with a high TNC level and is not very sensitive to a high level of phenolic compounds.

  20. The Ciidae (Coleoptera) of New Brunswick, Canada: New records and new synonyms. (United States)

    Lopes-Andrade, Cristiano; Webster, Reginald P; Webster, Vincent L; Alderson, Chantelle A; Hughes, Cory C; Sweeney, Jon D


    The Ciidae of New Brunswick, Canada are reviewed. Seventeen species are recorded for New Brunswick, including the following 10 species that are newly recorded for the province: Ceracis singularis (Dury), Ceracis thoracicornis (Ziegler), Cis angustus Hatch, Cis fuscipes Mellié, Cis horridulus Casey, Cis striatulus Mellié, Dolichocis laricinus (Mellié), Malacocis brevicollis (Casey), Orthocis punctatus (Mellié), and Plesiocis cribrum Casey. Additional locality data are provided for the following species previously known from the province: Cis americanus Mannerheim, Cis creberrimus Mellié, Cis levettei (Casey), Cis submicans Abeille de Perrin, Dolichocis manitoba Dury, Hadreule elongatula (Gyllenhal), and Octotemnus glabriculus (Gyllenhal). Seven synonyms are proposed here; Cis pistoria Casey with Cis submicans Abeille de Perrin; Cis fraternus Casey, Cis macilentus Casey and Cis striolatus Casey with Cis striatulus Mellié; Dolichocis indistinctus Hatch with Dolichocis laricinus (Mellié); and Octotemnus denudatus Casey and Octotemnus laevis Casey with Octotemnus glabriculus (Gyllenhal). Lindgren funnel traps provided the majority of specimens for 15 of the 17 species reported from New Brunswick and were the sole source of specimens for seven of the 10 species newly reported here, suggesting they are a very useful tool for sampling Ciidae in the forests of New Brunswick. PMID:27110172

  1. Multiple independent fusions of glucose-6-phosphate dehydrogenase with enzymes in the pentose phosphate pathway.

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    Nicholas A Stover

    Full Text Available Fusions of the first two enzymes in the pentose phosphate pathway, glucose-6-phosphate dehydrogenase (G6PD and 6-phosphogluconolactonase (6PGL, have been previously described in two distant clades, chordates and species of the malarial parasite Plasmodium. We have analyzed genome and expressed sequence data from a variety of organisms to identify the origins of these gene fusion events. Based on the orientation of the domains and range of species in which homologs can be found, the fusions appear to have occurred independently, near the base of the metazoan and apicomplexan lineages. Only one of the two metazoan paralogs of G6PD is fused, showing that the fusion occurred after a duplication event, which we have traced back to an ancestor of choanoflagellates and metazoans. The Plasmodium genes are known to contain a functionally important insertion that is not seen in the other apicomplexan fusions, highlighting this as a unique characteristic of this group. Surprisingly, our search revealed two additional fusion events, one that combined 6PGL and G6PD in an ancestor of the protozoan parasites Trichomonas and Giardia, and another fusing G6PD with phosphogluconate dehydrogenase (6PGD in a species of diatoms. This study extends the range of species known to contain fusions in the pentose phosphate pathway to many new medically and economically important organisms.

  2. Revisiting Myosin Families Through Large-scale Sequence Searches Leads to the Discovery of New Myosins. (United States)

    Pasha, Shaik Naseer; Meenakshi, Iyer; Sowdhamini, Ramanathan


    Myosins are actin-based motor proteins involved in many cellular movements. It is interesting to study the evolutionary patterns and the functional attributes of various types of myosins. Computational search algorithms were performed to identify putative myosin members by phylogenetic analysis, sequence motifs, and coexisting domains. This study is aimed at understanding the distribution and the likely biological functions of myosins encoded in various taxa and available eukaryotic genomes. We report here a phylogenetic analysis of around 4,064 myosin motor domains, built entirely from complete or near-complete myosin repertoires incorporating many unclassified, uncharacterized sequences and new myosin classes, with emphasis on myosins from Fungi, Haptophyta, and other Stramenopiles, Alveolates, and Rhizaria (SAR). The identification of large classes of myosins in Oomycetes, Cellular slime molds, Choanoflagellates, Pelagophytes, Eustigmatophyceae, Fonticula, Eucoccidiorida, and Apicomplexans with novel myosin motif variants that are conserved and thus presumably functional extends our knowledge of this important family of motor proteins. This work provides insights into the distribution and probable function of myosins including newly identified myosin classes. PMID:27597808

  3. Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing Precambrian fossil record of siliceous sponge spicules (United States)

    Sperling, E. A.; Robinson, J.; Pisani, D.; Peterson, K.


    The earliest evidence for animal life comes from the fossil record of 24-isopropylcholestane, a sterane found in Cryogenian deposits, and whose precursors are found in modern demosponges, but not choanoflagellates, calcareans, hexactinellids, or eumetazoans. However, many modern demosponges are also characterized by the presence of siliceous spicules, and there are no convincing demosponge spicules in strata older than the Cambrian. This temporal disparity highlights a problem with our understanding of the Precambrian fossil record - either these supposed demosponge-specific biomarkers were derived from the sterols of some other organism and are simply retained in modern demosponges, or spicules do not primitively characterize crown-group demosponges. Resolving this issue requires resolving the phylogenetic placement of another group of sponges, the hexactinellids, which not only make a spicule thought to be homologous to the spicules of demosponges, but also make their first appearance near the Precambrian/Cambrian boundary. Using two independent analytical approaches and data sets - traditional molecular phylogenetic analyses and the presence or absence of specific microRNA genes - we show that demosponges are monophyletic, and that hexactinellids are their sister group (together forming the Silicea). Thus, spicules must have evolved before the last common ancestor of all living siliceans, suggesting the presence of a significant gap in the silicean spicule fossil record. Molecular divergence estimates date the origin of this last common ancestor well within the Cryogenian, consistent with the biomarker record, and strongly suggests that siliceous spicules were present during the Precambrian but were not preserved.

  4. Evolutionary relationships of Metazoa within the eukaryotes based on molecular data from Porifera. (United States)

    Schütze, J; Krasko, A; Custodio, M R; Efremova, S M; Müller, I M; Müller, W E


    Recent molecular data provide strong support for the view that all metazoan phyla, including Porifera, are of monophyletic origin. The relationship of Metazoa, including the Porifera, to Plantae, Fungi and unicellular eukaryotes has only rarely been studied by using cDNAs coding for proteins. Sequence data from rDNA suggested a relationship of Porifera to unicellular eukaryotes (choanoflagellates). However, ultrastructural studies of choanocytes did not support these findings. In the present study, we compared amino acid sequences that are found in a variety of metazoans (including sponges) with those of Plantae, Fungi and unicellular eukaryotes, to obtain an answer to this question. We used the four sequences from 70 kDa heat-shock proteins, the serine-threonine kinase domain found in protein kinases, beta-tubulin and calmodulin. The latter two sequences were deduced from cDNAs, isolated from the sponge Geodia cydonium for the phylogenetic analyses presented. These revealed that the sponge molecules were grouped into the same branch as the Metazoa, which is statistically (significantly) separated from those branches that comprise the sequences from Fungi, Plantae and unicellular eukaryotes. From our molecular data it seems evident that the unicellular eukaryotes existed at an earlier stage of evolution, and the Plantae and especially the Fungi and the Metazoa only appeared later. PMID:10081159

  5. Functional Characterization of Cnidarian HCN Channels Points to an Early Evolution of Ih.

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    Emma C Baker

    Full Text Available HCN channels play a unique role in bilaterian physiology as the only hyperpolarization-gated cation channels. Their voltage-gating is regulated by cyclic nucleotides and phosphatidylinositol 4,5-bisphosphate (PIP2. Activation of HCN channels provides the depolarizing current in response to hyperpolarization that is critical for intrinsic rhythmicity in neurons and the sinoatrial node. Additionally, HCN channels regulate dendritic excitability in a wide variety of neurons. Little is known about the early functional evolution of HCN channels, but the presence of HCN sequences in basal metazoan phyla and choanoflagellates, a protozoan sister group to the metazoans, indicate that the gene family predates metazoan emergence. We functionally characterized two HCN channel orthologs from Nematostella vectensis (Cnidaria, Anthozoa to determine which properties of HCN channels were established prior to the emergence of bilaterians. We find Nematostella HCN channels share all the major functional features of bilaterian HCNs, including reversed voltage-dependence, activation by cAMP and PIP2, and block by extracellular Cs+. Thus bilaterian-like HCN channels were already present in the common parahoxozoan ancestor of bilaterians and cnidarians, at a time when the functional diversity of voltage-gated K+ channels was rapidly expanding. NvHCN1 and NvHCN2 are expressed broadly in planulae and in both the endoderm and ectoderm of juvenile polyps.

  6. Metabolic and chaperone gene loss marks the origin of animals: evidence for Hsp104 and Hsp78 chaperones sharing mitochondrial enzymes as clients.

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    Albert J Erives

    Full Text Available The evolution of animals involved acquisition of an emergent gene repertoire for gastrulation. Whether loss of genes also co-evolved with this developmental reprogramming has not yet been addressed. Here, we identify twenty-four genetic functions that are retained in fungi and choanoflagellates but undetectable in animals. These lost genes encode: (i sixteen distinct biosynthetic functions; (ii the two ancestral eukaryotic ClpB disaggregases, Hsp78 and Hsp104, which function in the mitochondria and cytosol, respectively; and (iii six other assorted functions. We present computational and experimental data that are consistent with a joint function for the differentially localized ClpB disaggregases, and with the possibility of a shared client/chaperone relationship between the mitochondrial Fe/S homoaconitase encoded by the lost LYS4 gene and the two ClpBs. Our analyses lead to the hypothesis that the evolution of gastrulation-based multicellularity in animals led to efficient extraction of nutrients from dietary sources, loss of natural selection for maintenance of energetically expensive biosynthetic pathways, and subsequent loss of their attendant ClpB chaperones.

  7. The Evolution of Extracellular Matrix (United States)

    Özbek, Suat; Balasubramanian, Prakash G.; Chiquet-Ehrismann, Ruth; Tucker, Richard P.


    We present a perspective on the molecular evolution of the extracellular matrix (ECM) in metazoa that draws on research publications and data from sequenced genomes and expressed sequence tag libraries. ECM components do not function in isolation, and the biological ECM system or “adhesome” also depends on posttranslational processing enzymes, cell surface receptors, and extracellular proteases. We focus principally on the adhesome of internal tissues and discuss its origins at the dawn of the metazoa and the expansion of complexity that occurred in the chordate lineage. The analyses demonstrate very high conservation of a core adhesome that apparently evolved in a major wave of innovation in conjunction with the origin of metazoa. Integrin, CD36, and certain domains predate the metazoa, and some ECM-related proteins are identified in choanoflagellates as predicted sequences. Modern deuterostomes and vertebrates have many novelties and elaborations of ECM as a result of domain shuffling, domain innovations and gene family expansions. Knowledge of the evolution of metazoan ECM is important for understanding how it is built as a system, its roles in normal tissues and disease processes, and has relevance for tissue engineering, the development of artificial organs, and the goals of synthetic biology. PMID:21160071

  8. Evolution of the sex-related locus and genomic features shared in microsporidia and fungi.

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    Soo Chan Lee

    Full Text Available BACKGROUND: Microsporidia are obligate intracellular, eukaryotic pathogens that infect a wide range of animals from nematodes to humans, and in some cases, protists. The preponderance of evidence as to the origin of the microsporidia reveals a close relationship with the fungi, either within the kingdom or as a sister group to it. Recent phylogenetic studies and gene order analysis suggest that microsporidia share a particularly close evolutionary relationship with the zygomycetes. METHODOLOGY/PRINCIPAL FINDINGS: Here we expanded this analysis and also examined a putative sex-locus for variability between microsporidian populations. Whole genome inspection reveals a unique syntenic gene pair (RPS9-RPL21 present in the vast majority of fungi and the microsporidians but not in other eukaryotic lineages. Two other unique gene fusions (glutamyl-prolyl tRNA synthetase and ubiquitin-ribosomal subunit S30 that are present in metazoans, choanoflagellates, and filasterean opisthokonts are unfused in the fungi and microsporidians. One locus previously found to be conserved in many microsporidian genomes is similar to the sex locus of zygomycetes in gene order and architecture. Both sex-related and sex loci harbor TPT, HMG, and RNA helicase genes forming a syntenic gene cluster. We sequenced and analyzed the sex-related locus in 11 different Encephalitozoon cuniculi isolates and the sibling species E. intestinalis (3 isolates and E. hellem (1 isolate. There was no evidence for an idiomorphic sex-related locus in this Encephalitozoon species sample. According to sequence-based phylogenetic analyses, the TPT and RNA helicase genes flanking the HMG genes are paralogous rather than orthologous between zygomycetes and microsporidians. CONCLUSION/SIGNIFICANCE: The unique genomic hallmarks between microsporidia and fungi are independent of sequence based phylogenetic comparisons and further contribute to define the borders of the fungal kingdom and support the

  9. Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions

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    Aruga Jun


    Full Text Available Abstract Background The C2H2 zinc finger (ZF domain is widely conserved among eukaryotic proteins. In Zic/Gli/Zap1 C2H2 ZF proteins, the two N-terminal ZFs form a single structural unit by sharing a hydrophobic core. This structural unit defines a new motif comprised of two tryptophan side chains at the center of the hydrophobic core. Because each tryptophan residue is located between the two cysteine residues of the C2H2 motif, we have named this structure the tandem CWCH2 (tCWCH2 motif. Results Here, we characterized 587 tCWCH2-containing genes using data derived from public databases. We categorized genes into 11 classes including Zic/Gli/Glis, Arid2/Rsc9, PacC, Mizf, Aebp2, Zap1/ZafA, Fungl, Zfp106, Twincl, Clr1, and Fungl-4ZF, based on sequence similarity, domain organization, and functional similarities. tCWCH2 motifs are mostly found in organisms belonging to the Opisthokonta (metazoa, fungi, and choanoflagellates and Amoebozoa (amoeba, Dictyostelium discoideum. By comparison, the C2H2 ZF motif is distributed widely among the eukaryotes. The structure and organization of the tCWCH2 motif, its phylogenetic distribution, and molecular phylogenetic analysis suggest that prototypical tCWCH2 genes existed in the Opisthokonta ancestor. Within-group or between-group comparisons of the tCWCH2 amino acid sequence identified three additional sequence features (site-specific amino acid frequencies, longer linker sequence between two C2H2 ZFs, and frequent extra-sequences within C2H2 ZF motifs. Conclusion These features suggest that the tCWCH2 motif is a specialized motif involved in inter-zinc finger interactions.

  10. Nme gene family evolutionary history reveals pre-metazoan origins and high conservation between humans and the sea anemone, Nematostella vectensis.

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    Thomas Desvignes

    Full Text Available BACKGROUND: The Nme gene family is involved in multiple physiological and pathological processes such as cellular differentiation, development, metastatic dissemination, and cilia functions. Despite the known importance of Nme genes and their use as clinical markers of tumor aggressiveness, the associated cellular mechanisms remain poorly understood. Over the last 20 years, several non-vertebrate model species have been used to investigate Nme functions. However, the evolutionary history of the family remains poorly understood outside the vertebrate lineage. The aim of the study was thus to elucidate the evolutionary history of the Nme gene family in Metazoans. METHODOLOGY/PRINCIPAL FINDINGS: Using a total of 21 eukaryote species including 14 metazoans, the evolutionary history of Nme genes was reconstructed in the metazoan lineage. We demonstrated that the complexity of the Nme gene family, initially thought to be restricted to chordates, was also shared by the metazoan ancestor. We also provide evidence suggesting that the complexity of the family is mainly a eukaryotic innovation, with the exception of Nme8 that is likely to be a choanoflagellate/metazoan innovation. Highly conserved gene structure, genomic linkage, and protein domains were identified among metazoans, some features being also conserved in eukaryotes. When considering the entire Nme family, the starlet sea anemone is the studied metazoan species exhibiting the most conserved gene and protein sequence features with humans. In addition, we were able to show that most of the proteins known to interact with human NME proteins were also found in starlet sea anemone. CONCLUSION/SIGNIFICANCE: Together, our observations further support the association of Nme genes with key cellular functions that have been conserved throughout metazoan evolution. Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of

  11. Megaphylogeny, cell body plans, adaptive zones: causes and timing of eukaryote basal radiations. (United States)

    Cavalier-Smith, Thomas


    I discuss eukaryote megaphylogeny and the timing of major innovations in the light of multigene trees and the rarity of marine/freshwater evolutionary transitions. The first eukaryotes were aerobic phagotrophs, probably substratum-associated heterotrophic amoeboflagellates. The primary eukaryote bifurcation generated unikonts (ancestrally probably unicentriolar, with a conical microtubular [MT] cytoskeleton) and bikonts (ciliary transformation from anterior cilium to ancestrally gliding posterior cilium; cytoskeleton of ventral MT bands). Unikonts diverged into Amoebozoa with anterior cilia, lost when lobosan broad pseudopods evolved for locomotion, and Choanozoa with posterior cilium and filose pseudopods that became unbranched tentacles/microvilli in holozoa and eventually the choanoflagellate/choanocyte collar. Of choanozoan ancestry, animals evolved epithelia, fibroblasts, eggs, and sperm. Fungi and Ichthyosporea evolved walls. Bikonts, ancestrally with ventral grooves, include three adaptively divergent megagroups: Rhizaria (Retaria and Cercozoa, ancestrally reticulofilose soft-surfaced gliding amoeboflagellates), and the originally planktonic Excavata, and the corticates (Plantae and chromalveolates) that suppressed pseudopodia. Excavata evolved cilia-generated feeding currents for grooval ingestion; corticates evolved cortical alveoli and ciliary hairs. Symbiogenetic origin and transfers of chloroplasts stimulated an explosive radiation of corticates--hard to resolve on multigene trees--and opisthokonts, and ensuing Cambrian explosions of animals and protists. Plantae lost phagotrophy and multiply evolved walls and macroalgae. Apusozoa, with dorsal pellicle and ventral pseudopods, are probably the most divergent bikonts or related to opisthokonts. Eukaryotes probably originated 800-850 My ago. Amoebozoa, Apusozoa, Loukozoa, and Metamonada may be the only extant eukaryote phyla pre-dating Neoproterozoic snowball earth. New subphyla are established for

  12. A molecular timescale of eukaryote evolution and the rise of complex multicellular life

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    Venturi Maria L


    Full Text Available Abstract Background The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. Results Our phylogenetic analyses revealed that (i animals are more closely related to fungi than to plants, (ii red algae are closer to plants than to animals or fungi, (iii choanoflagellates are closer to animals than to fungi or plants, (iv diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v diplomonads are basal to other eukaryotes (including alveolates and euglenozoans. Divergence times were estimated from global and local clock methods using 20–188 proteins per node, with data treated separately (multigene and concatenated (supergene. Different time estimation methods yielded similar results (within 5%: vertebrate-arthropod (964 million years ago, Ma, Cnidaria-Bilateria (1,298 Ma, Porifera-Eumetozoa (1,351 Ma, Pyrenomycetes-Plectomycetes (551 Ma, Candida-Saccharomyces (723 Ma, Hemiascomycetes-filamentous Ascomycota (982 Ma, Basidiomycota-Ascomycota (968 Ma, Mucorales-Basidiomycota (947 Ma, Fungi-Animalia (1,513 Ma, mosses-vascular plants (707 Ma, Chlorophyta-Tracheophyta (968 Ma, Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma, Plantae-Animalia (1,609 Ma, Alveolata-plants+animals+fungi (1,973 Ma, Euglenozoa-plants+animals+fungi (1,961 Ma, and Giardia-plants+animals+fungi (2,309 Ma. By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to ~10

  13. Phylogeny and evolution of Rab7 and Rab9 proteins

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    Wyroba Elżbieta


    Full Text Available Abstract Background An important role in the evolution of intracellular trafficking machinery in eukaryotes played small GTPases belonging to the Rab family known as pivotal regulators of vesicle docking, fusion and transport. The Rab family is very diversified and divided into several specialized subfamilies. We focused on the VII functional group comprising Rab7 and Rab9, two related subfamilies, and analysed 210 sequences of these proteins. Rab7 regulates traffic from early to late endosomes and from late endosome to vacuole/lysosome, whereas Rab9 participates in transport from late endosomes to the trans-Golgi network. Results Although Rab7 and Rab9 proteins are quite small and show heterogeneous rates of substitution in different lineages, we found a phylogenetic signal and inferred evolutionary relationships between them. Rab7 proteins evolved before radiation of main eukaryotic supergroups while Rab9 GTPases diverged from Rab7 before split of choanoflagellates and metazoans. Additional duplication of Rab9 and Rab7 proteins resulting in several isoforms occurred in the early evolution of vertebrates and next in teleost fishes and tetrapods. Three Rab7 lineages emerged before divergence of monocots and eudicots and subsequent duplications of Rab7 genes occurred in particular angiosperm clades. Interestingly, several Rab7 copies were identified in some representatives of excavates, ciliates and amoebozoans. The presence of many Rab copies is correlated with significant differences in their expression level. The diversification of analysed Rab subfamilies is also manifested by non-conserved sequences and structural features, many of which are involved in the interaction with regulators and effectors. Individual sites discriminating different subgroups of Rab7 and Rab9 GTPases have been identified. Conclusion Phylogenetic reconstructions of Rab7 and Rab9 proteins were performed by a variety of methods. These Rab GTPases show diversification

  14. The kingdom Protista and its 45 phyla. (United States)

    Corliss, J O


    . Chytridiomycota Sparrow, 1959). III. The chlorobionts (Chlorophyta Pascher, 1914; Prasinophyta Christensen, 1962; Conjugatophyta Engler, 1892; Charophyta Rabenhorst, 1863; incert. sed. Glaucophyta Bohlin, 1901). IV. The euglenozoa (Euglenophyta Pascher, 1931; Kinetoplastidea Honigberg, 1963; incert. sed. Pseudociliata Corliss & Lipscomb, 1982). V. The rhodophytes (Rhodophyta Rabenhorst, 1863). VI. The cryptomonads (Cryptophyta Pascher, 1914). VII. The choanoflagellates (Choanoflagellata Kent, 1880).(ABSTRACT TRUNCATED AT 400 WORDS) PMID:6395918

  15. Contribuição ao estudo das malformações occipito-cervical, particularmente da impressão basilar

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    Horacio M. Canelas


    Full Text Available The authors outline the development of the spine and skull, particularly of axis, atlas and occipital bone. As neuro-skeletal dysmorphisms, the occipito-cervical malformations belong to the neurodysplastic group. They are classified as skeletal anomalies, associated nervous malformations and meningeal reactions. Vertebralization of the occipital bone and occipitalization of atlas, subluxation of odontoid process, dysplasia of the occipital bone, dystrophia brevicollis and other anomalies are discussed. Special care is given to the study of basilar impression; its concept, history, incidence, clinical and neurological symptoms, radiological characterization (craniographic, perimyelographic and iodoventriculographic aspects and surgical treatment are reviewed. The authors report five cases of occipito-cervical malformations, which are the first references in Brazilian literature. In case 1 the anomalies (manifestation of occipital vertebra and Arnold-Chiari deformity were disclosed at an operation for cisticercosis of the posterior fossa. In the following four cases invagination of the basilar portion of the occipital bone (basilar impression could be radiologically demonstrated; in case 2 a suboccipital craniectomy and a laminectomy of atlas and axis were performed but the patient died a week later and the necroscopic examination confirmed the neuro-skeletal anomalies. In all cases there were several associated malformations. In case 2 there were occipitalization of the atlas, fusion of the first and second cervical vertebrae, supernumerary rib of the seventh cervical vertebra, supernumerary lumbar vertebra, and Arnold-Chiari deformity; at necropsy it was found a syringomyelic cyst on the cervical cord and a fibrous dural ring over the foramen magnum. Case 3 showed the syndrome of Klippel-Feil, besides supernumerary ribs of the seventh cervical and first dorsal vertebrae, Arnold-Chiari malfotmation and probable aplasia of cell groups in the

  16. Resolving the Divergence Times and Major Evolutionary Relationships of Protoctists%原生生物物种分歧时间和主要演化关系的定量计算

    Institute of Scientific and Technical Information of China (English)



    The divergence times and evolutionary relationships of some major protoctist clades were resolved by equation for molecular absolute evolutionary rates and several protein molecules:EF-1α,EF-2,NADH1 and CytB.The results showed that protoctists evolved from the route as:algae→fungi→protozoan.Their respective evolutionary routes are:(1) After the seperation of red algae at 1.331 Ga ago,the green algae separated from it around 1.1744 Ga ago, Mosses seperated at 0.4527 Ga ago,ferns seperated at 0.437 Ga ago.The divergence times of club-mosses,liverworts, Chlamydomonadales and Chlorellales are 0.4185,0.4457,0.5202 and 0.5239 Ga ago,respectively;(2) both Slime molds and oomycetes belonge to Fungi evolutionary branch,which separated about 1.0456 and 0.9032 Ga ago;(3) In protozoan branch,Apicomplexa and Choanoflagellates separated about 1.045 and 0.8122 Ga ago,respectively.Our results agreed well with the references work based on fossil records,and provided a new way to precisely resolve the evolutionary relationships of all protoctists.%使用本文作者提出的分子绝对进化速率的计算公式和EF-1α,EF-2,NADH1和CytB等蛋白质分子,对原生生物的一些主要类群:藻类、真菌和原生动物的物种分歧时间和演化关系进行了定量计算.结果显示,原核生物沿着藻类→真菌→原生动物的方向演化.它们的演化关系为:(1)红藻自13.31亿年前分化出后,于11.74亿年前分化出绿藻,绿藻于4.527亿年前分化出藓类,4.37亿年前分化出蕨类;其他物种如石松类、肝苔类、团藻和小球藻分别于4.185亿年前、4.457亿年前、5.202亿年前和5.239亿年前分化出;(2)黏菌和卵菌均属于真菌进化分枝,分别于10.456亿年前和9.032亿年前分化出;(3)原生动物进化分枝中于10.45亿年前分化出孢子虫等,8.122亿年前领鞭毛虫与多细胞动物分化.这些结果均与基于化石记录的文献报道相符.

  17. Review of the genus Chalcolepidius Eschscholtz, 1829 (Coleoptera, Elateridae, Agrypninae

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    Sônia Aparecida Casari


    Full Text Available The genus Chalcolepidius is revised. Type specimens of 65 nominal species, except C. costatus Pjatakowa, 1941, C. fleutiauxi Pjatakowa, 1941 and C. viriditarsus Schwarz, 1906, are examined. Eighty five species are studied, of which 34 are synonymyzed and 12 new species described; three species, C. alicii Pjatakowa, 1941, C. haroldi Candèze, 1878 and C. unicus Fleutiaux, 1910, formely included in this genus, are not congeneric and are removed; C. validus Candèze, 1857 is revalidated. The genus is now formed by 63 species. Redescriptions, illustrations and a key for the examined species, and a cladistic analysis for groups of species are also included. New synonyms established: C. apacheanus Casey, 1891 = C. simulans Casey, 1907 syn. nov. = C. acuminatus Casey, 1907 syn. nov. = C. nobilis Casey, 1907 syn. nov.; C. approximatus Erichson, 1841 = C. aztecus Casey, 1907 syn. nov. = C. niger Pjatakowa, 1941 syn. nov.; C. attenuatus Erichson, 1841 = C. cuneatus Champion, 1894 syn. nov. = C. tenuis Champion, 1894 syn. nov.; C. aurulentus Candèze, 1874 = C. candezei Dohrn, 1881 syn. nov. = C. grossheimi Pjatakowa, 1941 syn. nov.; C. bomplandii Guérin, 1844 = C. humboldti Candèze, 1881 syn. nov.; C. chalcantheus Candèze, 1857 = C. violaceous Pjatakowa, 1941 syn. nov.; C. cyaneus Candèze, 1881 = C. scitus Candèze, 1889 syn. nov. = C. abbreviatovittatus Pjatakowa, 1941 syn. nov.; C. desmarestii Chevrolat, 1835 = C. brevicollis Casey, 1907 syn. nov.; C. gossipiatus Guérin, 1844 = C. erichsonii Guérin-Méneville, 1844 syn. nov. = C. lemoinii Candèze, 1857 syn. nov.; C. inops Candèze, 1886 = C. murinus Champion, 1894 syn. nov.; C. jansoni Candèze, 1874 = C. mucronatus Candèze, 1889 syn. nov.; C. lacordairii Candèze, 1857 = C. exquisitus Candèze, 1886 syn. nov. = C. monachus Candèze, 1893 syn. nov.; C. lenzi Candèze, 1886 = C. behrensi Candèze, 1886 syn. nov.; C. oxydatus Candèze, 1857 = C. jekeli Candèze, 1874 syn. nov.; C. porcatus