Varnika Mittal1, Robert W Reid2, Denis Jacob Machado2, Vladimir Mashanov3, Daniel A Janies2. 1. Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA. vmittal@uncc.edu. 2. Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA. 3. Wake Forest Institute for Regenerative Medicine, 91 Technology Way NE, Winston-Salem, NC, 27101, USA.
Abstract
BACKGROUND: Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. RESULTS: The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. CONCLUSION: EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
BACKGROUND: Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. RESULTS: The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. CONCLUSION: EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
Authors: Gregorio V Linchangco; David W Foltz; Rob Reid; John Williams; Conor Nodzak; Alexander M Kerr; Allison K Miller; Rebecca Hunter; Nerida G Wilson; William J Nielsen; Christopher L Mah; Greg W Rouse; Gregory A Wray; Daniel A Janies Journal: Mol Phylogenet Evol Date: 2017-07-27 Impact factor: 4.286
Authors: Phillip L Davidson; Haobing Guo; Lingyu Wang; Alejandro Berrio; He Zhang; Yue Chang; Andrew L Soborowski; David R McClay; Guangyi Fan; Gregory A Wray Journal: Genome Biol Evol Date: 2020-07-01 Impact factor: 3.416
Authors: Daniel A Janies; Zach Witter; Gregorio V Linchangco; David W Foltz; Allison K Miller; Alexander M Kerr; Jeremy Jay; Robert W Reid; Gregory A Wray Journal: BMC Bioinformatics Date: 2016-01-22 Impact factor: 3.169
Authors: Vladimir Mashanov; Jennifer Akiona; Maleana Khoury; Jacob Ferrier; Robert Reid; Denis Jacob Machado; Olga Zueva; Daniel Janies Journal: PLoS One Date: 2020-05-12 Impact factor: 3.240