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Background: Echinoderms are established models in experimental and developmental biology, however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging model organism in the field of regenerative biology. This new genomic resource provides a reference for experimental studies of regenerative mechanisms. Results: We report a de novo nuclear genome assembly for the brittle star O. brevispinum and annotation facilitated by the transcriptome assembly. The final assembly is 2.68 Gb in length and contains 146,703 predicted protein-coding gene models. We also report a mitochondrial genome for this species, which is 15,831 bp in length, and contains 13 protein-coding, 22 tRNAs, and 2 rRNAs genes, respectively. In addition, 29 genes of the Notch signaling pathway are identified to illustrate the practical utility of the assembly for studies of regeneration. Conclusions: The sequenced and annotated genome of O. brevispinum presented here provides the first such resource for an ophiuroid model species. Considering the remarkable regenerative capacity of this species, this genome will be an essential resource in future research efforts on molecular mechanisms regulating regeneration. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • 17 mtDNA genomes spanning Ophiuroidea used to explore phylogeny and gene order evolution. • mtDNA data support monophyletic Ophintegrida and Euryophiurida. • Only 3 mtDNA gene order arrangements observed and all sampled Euryalida with same order. • Euryalid gene order likely ancestral for Ophiuroidea. Abstract Brittle stars are conspicuous members of benthic ecosystems, fill many ecological niches and are the most speciose of all classes of echinoderms. With high levels of biodiversity, elucidating the evolutionary history of this group is important. Understanding of higher-level relationships within Ophiuroidea has been aided by multilocus nuclear data and DNA barcoding. However, the degree of consistency between mitochondrial and nuclear data within ophiuroids remains unclear and deserves further assessment. In this study, 17 mitochondrial genomes spanning the taxonomic breadth of Ophiuroidea were utilized to explore evolutionary relationships through maximum likelihood analyses, Bayesian inference and comparative assessment of gene order. Our phylogenetic analyses, based on both nucleotide and amino acid residues, support recent findings based on multilocus nuclear data and morphology, in that the brittle star clades Ophintegrida and Euryophiurida were recovered as monophyletic with the latter comprising Euyalida, Ophiuridae and Ophiopyrgidae. Only three different arrangements of the 13 protein coding and 2 ribosomal RNA genes were observed. As expected, tRNA genes were more likely to have undergone rearrangement but the order of all 37 genes was found to be conserved in all sampled Euryalida and Ophiuridae. Both Euryalida and the clade comprised of Ophiuridae and Ophiopyrgidae, each had their own conserved rearrangement of protein coding genes and ribosomal genes, after divergence from their last common ancestor. Euryalida has a rearrangement of the two ribosomal RNA genes, rrnS and rrnL , in contrast to Ophiuridae and Ophiopyrgidae, which had an inversion of the genes nad1 , nad2 , and cob relative to Ophintegrida. Further, our data support the gene order found in all sampled Euryalida as the most likely ancestral order for all Ophiuroidea. [ABSTRACT FROM AUTHOR]

Mitochondrial genomes provide an additional data source for nuclear phylogenomics. Recently, the taxonomic classification of Ophiuroidea was changed dramatically based on a molecular phylogenetic analysis that utilized a huge nuclear dataset of transcriptome and target-capture approaches. However, the mitochondrial genome analysis of Ophiuroidea was not conducted sufficiently in depth to allow comparison with current phylogenetic relationships, especially for the Ophintegrida. In this study, eight mitogenomes were newly reported in Amphilepidida and Ophiacanthida. Phylogenetic analyses were undertaken based on the nucleotide sequences of 13 protein coding genes (PCGs), 22 tRNA, and two rRNA, and the amino acid translated sequences of 13 PCGs. The results of the phylogenetic analysis suggested that the amino acid translated sequences were more useful than the nucleotide sequences for the analysis of higher phylogenetic relationships. The mitochondrial gene order of 13 PCGs and two rRNA in Amphilepidida and Ophiacanthida was relatively conserved. However, more complex gene orders occurred in the phylogeny of Amphilepidida and Ophiacanthida, including 22 tRNA. The results of our study suggest that Ophiuroidea has undergone more complex gene rearrangements than other classes of echinoderms. [ABSTRACT FROM AUTHOR]

Background: Brittle stars (Ophiuroidea, Echinodermata) have been increasingly used in studies of animal behavior, locomotion, regeneration, physiology, and bioluminescence. The success of these studies directly depends on good working knowledge of the ophiuroid nervous system. Results: Here, we describe the arm nervous system at different levels of organization, including the microanatomy of the radial nerve cord and peripheral nerves, ultrastructure of the neural tissue, and localization of different cell types using specific antibody markers. We standardize the nomenclature of nerves and ganglia, and provide an anatomically accurate digital 3D model of the arm nervous system as a reference for future studies. Our results helped identify several general features characteristic to the adult echinoderm nervous system, including the extensive anatomical interconnections between the ectoneural and hyponeural components, neuroepithelial organization of the central nervous system, and the supporting scaffold of the neuroepithelium formed by radial glial cells. In addition, we provide further support to the notion that the echinoderm radial glia is a complex and diverse cell population. We also tested the suitability of a range of specific cell-type markers for studies of the brittle star nervous system and established that the radial glial cells are reliably labeled with the ERG1 antibodies, whereas the best neuronal markers are acetylated tubulin, ELAV, and synaptotagmin B. The transcription factor Brn1/2/4 - a marker of neuronal progenitors - is expressed not only in neurons, but also in a subpopulation of radial glia. For the first time, we describe putative ophiuroid proprioceptors associated with the hyponeural part of the central nervous system. Conclusions: Together, our data help establish both the general principles of neural architecture common to the phylum Echinodermata and the specific ophiuroid features. [ABSTRACT FROM AUTHOR]

Ophioconis claviculata sp. nov. is described on the basis of three specimens collected from Ryukyu Islands, southwestern, Japan. The new species is distinct in having: disc covered by granules; four, sometimes five flat, polygonal oral papillae on each side of jaw; broad and flat teeth with hyaline distal end; spiniform and conical arm spines, two times longer than the corresponding arm segment at the maximum length; oralmost arm spines on proximal portion of arms flattened and clavate; four tentacle scales on third tentacle pore; and ventral arm plate longer than wide, with concentrate lamellar striations. The new species was found under rocks of open water as well as in a dark and medium to low salinity (28 ppt) environment of submarine cave, suggesting that this species tolerate this specific condition. [ABSTRACT FROM AUTHOR]

The fiords of southwestern New Zealand may promote the existence of genetically divergent populations as a result of geological and ecological isolation. The ophiuroidAstrobrachion constrictumlives on black coral in these fiords, and is thought to have a relatively short pelagic larval duration that may limit dispersal among populations. Samples ofA. constrictumwere collected from seven sites (four fiords) in Fiordland. Analysis of the mitochondrial COI gene using single-stranded conformational polymorphism revealed eight haplotypes, representatives of which were sequenced. These included nine variable sites, none of which were phylogenetically informative.G-test and AMOVA revealed little structuring of samples within or among fiords, but there was evidence for reduced gene flow among the most geographically separated fiords. We conclude that fiords do not house relict populations from earlier glaciations, and that little differential sorting of haplotypes has occurred in the last 10,000 years. [ABSTRACT FROM PUBLISHER]

Ophiuroids were collected during the Singapore Biodiversity Workshop at Pulau Ubin in 2012. About 520 specimens were provisionally identified and 22 species of ophiuroids recognised. Fourteen species are new to Singapore waters. [ABSTRACT FROM AUTHOR]

Sea cucumbers (Holothuroidea) are known to host ectocommensal animals but echinoderm epibionts have never been reported nor their effects on hosts appraised quantitatively. At one location in New Caledonia, we found a high number of ophiuroids (Ophiothelacf.danae) and synaptid sea cucumbers (Synaptula mediaandSynaptulasp.) living on the bumpy external body wall of sea cucumbers,Stichopus herrmanni. Rates of midday sediment defecation (mean: 23 g h−1) and short-term displacements (mean: 60 cm h−1) by the hosts were not significantly affected by the number of echinoderm commensals they carried. The frequent relationships at the location suggest that such facultative commensalism between echinoderms could be more common than previously understood. Appreciable numbers of scaleworms, crabs and shrimps on the sea cucumbers show that sea cucumbers can act as hosts to echinoderms and other epibiotic taxa, bolstering the notion that they play important ecological roles in reef ecosystems. [ABSTRACT FROM PUBLISHER]