Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.

IF 2.2 3区生物学 Q3 GENETICS & HEREDITY

G3: Genes|Genomes|Genetics Pub Date : 2025-10-08 DOI:10.1093/g3journal/jkaf188

Lydia J M Fong, Bernadette D Johnson, Iulia Darolti, Benjamin A Sandkam, Judith E Mank

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Abstract

The Amazon guppy, Poecilia bifurca, is a small live-bearing fish. The close relatives Poecilia reticulata, Poecilia picta, and Poecilia 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, 5 of which show gene expression in guppy male germ cells.

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基因组报告：亚马逊孔比鱼（Poecilia bifurca）的基因组揭示了性染色体的保存和剂量补偿。

亚马逊孔雀鱼是一种小型的活鱼。近亲缘植物网麻、picta和parae均具有相同的性染色体系统，但在Y变性程度和X染色体剂量补偿程度上存在较大差异。为了确定双歧树是否具有相同的性染色体系统，我们构建了一个雌性（XX）基因组草图，PacBio HiFi数据覆盖率为55X，得到785 Mb的汇编，BUSCO完整性为94.4%。我们使用这个基因组，发现双歧树与近缘种具有相同的性染色体，并表现出明显的Y染色体退化。我们将其与RNA-Seq数据相结合，发现两性间X连锁基因的表达相似，表明双歧双歧树也表现出完整的X染色体剂量补偿。我们进一步鉴定了11个假定的autosome-to-Y基因复制，其中5个在孔雀鱼雄性生殖细胞中显示基因表达。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

G3: Genes|Genomes|Genetics GENETICS & HEREDITY-

CiteScore

5.10

自引率

3.80%

发文量

305

审稿时长

3-8 weeks

期刊介绍： G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.