Evolutionary context can clarify gene names: Teleosts as a case study

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 d...

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Bibliographic Details
Published in:BioEssays 2021-06, Vol.43 (6), p.e2000258-n/a
Main Authors: Gasanov, Eugene V., Jędrychowska, Justyna, Kuźnicki, Jacek, Korzh, Vladimir
Format: Article
Language:English
Subjects:
Criteria
Evolution
Gene duplication
gene naming
Genes
Genetics
Genomes
Naming
Nomenclature
ohnologs
orthologs
paralogs
Phenotypes
reference genome
Reproduction (copying)
spotted gar
Synteny
synteny‐based evolutionary approach
teleosts
Vertebrates
whole‐genome duplication
Zebrafish
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Summary: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. Also see the video here: https://youtu.be/UKNLa_TvSgY The ideal gene name reflects gene's evolutionary history; It is not always a case, in particular for the teleosts duplicated genes (ohnologs); These should be named referring to the ancestral unduplicated genome and synteny; The proposed ex silico evolutionary‐based systematic synteny approach could be instrumental in improving gene naming.
ISSN:0265-9247
1521-1878
DOI:10.1002/bies.202000258