EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

Autor: Robert Reid, Denis Jacob Machado, Varnika Mittal, Vladimir Mashanov, Daniel Janies
Rok vydání: 2022
Předmět:
Zdroj: BMC genomic data. 23(1)
ISSN: 2730-6844
Popis: This upload contains supplementary digital material for the manuscript entitled "EchinoDB: An update to the web-based application for genomic and transcriptomic data on Echinoderms." The manuscript was written by Varnika Mittal (ORCiD: 0000-0002-3033-4891), Robert W. Reid (ORCiD: 0000-0001-7125-7151), Denis Jacob Machado (ORCiD: 0000-0001-9858-4515), Vladimir Mashanov (ORCID: 0000-0001-6875-7518), and Daniel A. Janies (ORCiD: 0000-0002-7890-9906). The manuscript was made available first as a preprint in bioRxiv (https://doi.org/10.1101/2022.01.03.474134). ABSTRACT 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. 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. 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. FILES DESCRIPTION TABLE S1 (CSV): Raw reads from the various echinoderm species are available via the NCBI's SRA. FILE S1 (PDF): EchinoDB user manual. FILE S2 (PDF): Echinoid database (EchinoidDB) user manual. FILE S3 (PDF): Ophiuroid database (OphiuroidDB) user manual. FILE S4 (PDF): Source code (in R). We also provided the source codes as three R scripts (see FileS4_Source_Code_EchinoDB_app.R, FileS4_Source_Code_EchinoidDB_app.R, and FileS4_Source_Code_OphiuroidDB_app.R) CORRESPONDENCE V. Mittal: vmittal [AT] uncc [DOT] edu
This is the supplementary material (Additional files) corresponding to the manuscript entitled "EchinoDB: An update to the web-based application for genomic and transcriptomic data on Echinoderms." The first version of this manuscript was made available as a preprint on bioRxiv.
Databáze: OpenAIRE
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