NanoString nCounter copy number variation assay

The sex chromosomes often follow unusual evolutionary trajectories. In
particular, the sex-limited Y and W chromosomes frequently exhibit a small
but unusual gene content in numerous species, where many genes have
undergone massive gene amplification. The reasons for this remain elusive
with a number of recent studies implicating meiotic drive, sperm
competition, genetic drift and gene conversion in the expansion of gene
families. However, our understanding is primarily based on Y chromosome
studies, and the W chromosome has been largely overlooked. Here, we
conduct a comprehensive investigation into the abundance, variability, and
evolution of ampliconic genes on the W both across and within avian
species. We find a striking deficit of gene families on the duck W
chromosome, as well as conservation in W-linked gene copy number across
duck breeds, indicating that gene amplification may not be such a general
feature of sex chromosome evolution as Y studies would initially suggest.
Furthermore, we show that gene families have expanded independently in the
duck and chicken. In particular, using contrasts between modern chicken
and duck breeds selected for different female-specific selection regimes
and their wild ancestors, we investigate the factors driving the expansion
of HINTW, a prominent ampliconic gene family hypothesized to play a role
in female reproduction and oogenesis. While we find that HINTW is
ampliconic in both species, our results support a role of female-specific
selection in driving gene amplification in the chicken but not the duck,
challenging the assumption that HINTW is key for female fecundity across
the avian phylogeny.

性染色体往往遵循非常规的演化轨迹。具体而言，限性Y染色体与W染色体在众多物种中通常呈现出小型却异常的基因组成，其中诸多基因经历了大规模的基因扩增。目前该现象背后的成因仍不明朗，近期多项研究将基因家族扩张的诱因归结为减数分裂驱动（meiotic drive）、精子竞争、遗传漂变以及基因转换（gene conversion）。然而我们的认知主要基于Y染色体的相关研究，W染色体在很大程度上被忽视了。
本研究针对鸟类物种间及物种内W染色体上的扩增基因（ampliconic genes）的丰度、变异程度与演化模式开展了全面探究。研究发现鸭类W染色体上的基因家族存在显著缺失，且不同鸭品种间W连锁基因的拷贝数保持保守，这表明基因扩增或许并非如Y染色体研究最初所暗示的那样，是性染色体演化的普遍特征。此外，我们证实鸭与鸡的基因家族扩增事件彼此独立发生。
具体而言，我们通过对比针对不同雌性特异性选择策略的现代家鸡与家鸭品种，及其野生祖先，探究驱动HINTW基因家族扩增的诱因。HINTW是一类重要的扩增基因家族，此前被推测在雌性生殖与卵子发生（oogenesis）过程中发挥功能。尽管我们发现HINTW在两个物种中均为扩增基因家族，但研究结果支持雌性特异性选择驱动家鸡基因扩增这一结论，而在家鸭中并未观察到该现象，这对“HINTW是鸟类系统发育中雌性繁殖力关键调控因子”这一既有假设提出了挑战。