Genome analysis confirms sex chromosomes in Poecilia bifurca, indicating Y chromosome degeneration and dosage compensation.
The Amazon guppy, Poecilia bifurca, is a small live-bearing fish. The close relatives P. reticulata, P. picta, and P. parae all share the same sex chromosome system, but with substantial diversity in the degree of Y degeneration and the extent of X chromosome dosage compensation. In order to identify if P. bifurca shares the same sex chromosome system, we built a female (XX) draft genome with 55X coverage of PacBio HiFi data, resulting in a 785 Mb assembly with 94.4% BUSCO completeness. We used this genome and found that P. bifurca shares the same sex chromosomes as related species and shows substantial Y chromosome degeneration. We combined this with RNA-Seq data and found similar expression of X-linked genes between sexes, revealing that P. bifurca also exhibits complete X chromosome dosage compensation. We further identify 11 putative autosome-to-Y gene duplications, five of which show gene expression in guppy male germ cells.
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Fong et al. (2025) studied this question.
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