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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.jsp Database URL https://www.echinobase.org/.
5P41HD095831-03 Eunice Kennedy Shriver National Institute of Child Health and Human Development, ACI-1445606 National Science Foundation, ACI-1548562 National Science Foundation, ACI-1928147 National Science Foundation, P41 HD095831 NICHD NIH HHS
Figure 1. Flowchart describing the Echinobase nomenclature pipeline. Following processing by NCBI and the Echinobase orthology pipeline, gene identifiers are assigned depending on orthology relationships to humans.
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