Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution
Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution
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DOI：
10.1186/s13059-020-02097-x
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发表时间：
2020-07-19
期刊：
影响因子：
12.3
通讯作者：
White, Michael A.
中科院分区：
文献类型：
--
作者：
Peichel, Catherine L.;McCann, Shaugnessy R.;White, Michael A.
异型性染色体在不同物种中反复进化。抑制X和Y染色体之间的重组会导致Y染色体的退化。变性的进展尚不清楚，因为异型Y染色体的完整序列组合仅在少数具有高度退化性染色体的分类群中产生。在这里，我们描述了三棘棘鱼（Gasterosteus aculeatus） Y染色体的组装，它的年龄不到2600万年，处于退化的中间阶段。我们之前的研究发现，X染色体和Y染色体之间的非重组区在X染色体上的跨度约为17.5 Mb。结果我们将长读测序与基于hi - c的接近引导组装相结合，产生了15.87 Mb的Y染色体组装。我们的组装与90多个Y染色体BAC克隆的细胞遗传学图谱和Sanger序列一致。我们在Y染色体上发现了三个进化层，与我们之前的细胞遗传学分析确定的三个倒置一致。三棘棘鱼Y在保留单倍不足基因和积累睾丸偏倚表达基因方面表现出与更多退化性染色体的趋同，其中许多是最近的重复。然而，我们没有发现在其他性染色体系统中发现大扩增子的证据。我们还报道了主要性别决定基因的一个极好的候选者：Amh的易位拷贝（Amhy）。总之，我们的工作表明，形成性染色体的进化力量可以导致Y染色体整体遗传结构的相对快速变化。
Background Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. Results We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). Conclusions Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes.