Journal Article
Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes
Zhao, Q., Shao, F., Li, Y., Yi, S.V. and Peng, Z.
Record Number:
5972
Year:
2022
Journal:
Molecular Ecology
Pages:
yy
Volume:
xx
Notes:
This article has been accepted for publication and undergone full peer review but has not
been through the copyediting, typesetting, pagination and proofreading process which
may lead to differences between this version and the Version of Record
Abstract:
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits,
including the characteristic loss of eyes. To understand whether such phenotypic convergence
shares similar genomic bases, here, we investigated genome-wide evolutionary signatures of
cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and
their surface fish relatives. Notably, we newly sequenced and generated a whole-genome
assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several
shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their
surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω)
was significantly elevated in cavefishes compared to in surface fishes, consistent with the
relaxation of purifying selection. In addition, cavefish genomes had an increased mutational
load, including mutations that alter protein hydrophobicity profiles, which were considered
harmful. Interestingly, however, we found no overlap in positively selected genes among
different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not
caused by positive selection of the same sets of genes. Analyses of previously identified
candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to
the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish
genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work
reveals previously uncharacterized patterns of cavefish genome evolution and provides
comparative insights into the evolution of cave-associated phenotypic traits.
Keywords: cavefish, relaxed selection, evolutionary rate, mutation, phenotypic evolution
Times Cited:
1
Relevent Species:
Related Records:
Wu, He and Li (2005)
Linemacheilus wulong
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