Evolutionary context can clarify teleosts gene names

Abstract

SummaryThe initial convention to name genes relied on historical precedent, order in the human genome or mutants in model systems. However, partial duplication of genes in teleosts required naming the duplicated genes, so ohnologs adopted the ‘a’ or ‘b’ extension. Rapid advances in deciphering the zebrafish genome in relation to the human genome instituted naming genes in all other fish genomes in the convention of zebrafish. Unfortunately, some ohnologs and their resembling orthologs suffered from incorrect nomenclature, which created confusion in particular instances like establishing disease models. We sought to overcome this barrier by establishing the ex silico evolutionary-based systematic approach to naming the ohnologs in teleosts and other fish. We compared gene synteny using the spotted gar genome as the reference, which represents the unduplicated ancestral state. Using new criteria, we identified several hundreds of potentially misnamed ohnologs and validated manually several ohnologs as a proof pf principle. This may help to establish a standard naming practice resulting in the improved evolutionary-based gene nomenclature. This approach may help to identify and rename ohnologs in all relevant EMBL-EBI and NCBI databases starting from the zebrafish genome to avoid further proliferation of misleading information.