Abstract
Echinoderm embryos and larvae are prominent experimental model systems for studying developmental mechanisms. High-quality, assembled, annotated genome sequences are now available for several echinoderm species, including representatives from most classes. The increased availability of these data necessitates the development of a nomenclature that assigns universally interpretable gene symbols to echinoderm genes to facilitate cross-species comparisons of gene functions, both within echinoderms and across other phyla. This paper describes the implementation of an improved set of echinoderm gene nomenclature guidelines that both communicates meaningful orthology information in protein-coding gene symbols and names and establishes continuity with nomenclatures developed for major vertebrate model organisms, including humans. Differences between the echinoderm gene nomenclature guidelines and vertebrate guidelines are examined and explained. This nomenclature incorporates novel solutions to allow for several types of orthologous relationships, including the single echinoderm genes with multiple vertebrate co-orthologs that result from whole-genome-duplication events. The current version of the Echinoderm Gene Nomenclature Guidelines can be found at https://www.echinobase.org/gene/static/geneNomenclature.jspDatabase URL https://www.echinobase.org/
Highlights
Echinoderms have served as important experimental model systems in biology for more than a century, in the field of developmental biology [1,2,3,4,5]
The sequencing of echinoderm genomes began with the Sea Urchin Genome Sequencing Consortium (RRID:SCR_002841) [17], which resulted in genome assembly from the purple sea urchin (Strongylocentrotus purpuratus)
Three of the orthology tools outputs used in the current Echinobase orthology pipeline are provided from DRSC Integrative Ortholog Prediction Tool (DIOPT) [Inparanoid [41, 42], OMA [46] and Orthofinder [47]] that uses protein models derived from the S. purpuratus genome and those of numerous major model organisms [37, 38]
Summary
Echinoderms have served as important experimental model systems in biology for more than a century, in the field of developmental biology [1,2,3,4,5]. A core goal of this nomenclature system is to incorporate robust orthology relationships between echinoderm and human genes when assigning gene symbols and names.
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