Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay.,PLOS Genetics

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Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay.
PLOS Genetics ( IF 4.0 ) Pub Date : 2019-11-18 , DOI: 10.1371/journal.pgen.1008502
Kevin H-C Wei ₁ , Doris Bachtrog ₁

Affiliation

Male Drosophila typically have achiasmatic meiosis, and fusions between autosomes and the Y chromosome have repeatedly created non-recombining neo-Y chromosomes that degenerate. Intriguingly, Drosophila nasuta males recombine, but their close relative D. albomicans reverted back to achiasmy after evolving neo-sex chromosomes. Here we use genome-wide polymorphism data to reconstruct the complex evolutionary history of neo-sex chromosomes in D. albomicans and examine the effect of recombination and its cessation on the initiation of neo-Y decay. Population and phylogenomic analyses reveal three distinct neo-Y types that are geographically restricted. Due to ancestral recombination with the neo-X, overall nucleotide diversity on the neo-Y is similar to the neo-X but severely reduced within neo-Y types. Consistently, the neo-Y chromosomes fail to form a monophyletic clade in sliding window trees outside of the region proximal to the fusion. Based on tree topology changes, we inferred the recombination breakpoints that produced haplotypes specific to each neo-Y type. We show that recombination became suppressed at different time points for the different neo-Y haplotypes. Haplotype age correlates with onset of neo-Y decay, and older neo-Y haplotypes show more fixed gene disruption via frameshift indels and down-regulation of neo-Y alleles. Genes are downregulated independently on the different neo-Ys, but are depleted of testes-expressed genes across all haplotypes. This indicates that genes important for male function are initially shielded from degeneration. Our results offer a time course of the early progression of Y chromosome evolution, showing how the suppression of recombination, through the reversal to achiasmy in D. albomicans males, initiates the process of degeneration.

中文翻译：

果蝇白蚁的祖先雄性重组产生了地理上受限制的新Y染色体单倍型，该单倍型随着年龄和衰变的开始而变化。

雄性果蝇通常具有失弛缓性减数分裂，常染色体与Y染色体之间的融合已反复产生简并的非重组新Y染色体。有趣的是，果蝇nasuta雄性重组，但是它们的近亲白僵菌在进化了新性染色体后又恢复为裂口性。在这里，我们使用全基因组多态性数据来重建白僵菌中新性染色体的复杂进化历史，并研究重组及其停止对新Y衰变的启动的影响。种群和种系学分析揭示了三种不同的新Y型，它们在地理上受到限制。由于与neo-X的祖先重组，neo-Y上的总体核苷酸多样性与neo-X相似，但在neo-Y类型内严重降低。始终如一 neo-Y染色体无法在融合区附近区域的滑动窗口树中形成单系进化分支。根据树形拓扑的变化，我们推断出重组断点，这些重组断点产生了特定于每个neo-Y类型的单倍型。我们显示，重组在不同的时间点被抑制为不同的新Y型单倍型。单倍型年龄与新Y型衰变的发生有关，而较老的新Y型单倍型通过移码插入和新Y等位基因的下调显示更多固定的基因破坏。基因在不同的neo-Y上独立下调，但在所有单倍型中都缺失了睾丸表达的基因。这表明，对于男性功能重要的基因最初已被保护免受变性。我们的结果提供了Y染色体进化的早期进程的时间过程，

更新日期：2019-12-03

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