ZFIN ID: ZDB-PUB-210409-17
Evolutionary context can clarify gene names: Teleosts as a case study
Gasanov, E.V., Jędrychowska, J., Kuźnicki, J., Korzh, V.
Date: 2021
Source: BioEssays : news and reviews in molecular, cellular and developmental biology   43(6): e2000258 (Journal)
Registered Authors: Jędrychowska, Justyna, Korzh, Vladimir
Keywords: gene naming, ohnologs, orthologs, paralogs, reference genome, spotted gar, synteny, synteny-based evolutionary approach, teleosts, whole-genome duplication, zebrafish
MeSH Terms:
  • Animals
  • Biological Evolution
  • Evolution, Molecular*
  • Humans
  • Phylogeny
  • Synteny/genetics
  • Zebrafish*
PubMed: 33829511 Full text @ Bioessays
We developed an ex silico evolutionary-based systematic synteny approach to define and name the duplicated genes in vertebrates. The first convention for the naming of genes relied on historical precedent, the order in the human genome, and mutant phenotypes in model systems. However, total-genome duplication that resulted in teleost genomes required the naming of duplicated orthologous genes (ohnologs) in a specific manner. Unfortunately, as we review here, such naming has no defined criteria, and some ohnologs and their orthologs have suffered from incorrect nomenclature, thus creating confusion in comparative genetics and disease modeling. We sought to overcome this barrier by establishing an ex silico evolutionary-based systematic approach to naming ohnologs in teleosts. We developed software and compared gene synteny in zebrafish using the spotted gar genome as a reference, representing the unduplicated ancestral state. Using new criteria, we identified several hundred potentially misnamed ohnologs and validated the principle manually.