Supplementary Files S1 It contains the RepeatMasker annotation of the six avian genomes. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

学界长期观测到一类普遍模式：即便在全基因组重复序列含量较低的鸟类等物种中，限性染色体（Y和W染色体）的非重组区域所积累的重复序列丰度，也显著高于基因组其余区域。本研究针对性染色体高度异型的鸟类展开分析，结果显示其W染色体的转座因子（transposable element, TE）占比超过55%，而全基因组转座因子占比不足10%；该染色体同时承载了全基因组超过半数的全长（即具备潜在活性）内源性逆转录病毒（endogenous retroviruses, ERVs）。借助RNA测序（RNA-seq）与蛋白质质谱数据，我们成功检测到雌性特异性内源性逆转录病毒的表达特征信号。我们提出假说：鸟类W染色体可作为活性内源性逆转录病毒的庇护所，这大概率会导致雌性偏向的突变负荷，进而影响雌性生理机能，其效应类似果蝇中的‘毒性Y’（toxic-Y）效应。此外，霍尔丹法则（Haldane's rule）指出，异配性别个体的杂交后代生育能力会降低。我们认为，W染色体上活性内源性逆转录病毒的过量积累，可作为解释霍尔丹法则的额外变量——该现象可能通过杂交后代中转座因子与抑制因子的错配，引发物种间的遗传不相容性。综上，本研究结果表明，雌性特异性W染色体的序列组成所产生的影响，远不止性别决定与基因剂量调控两个方面。本文属于‘挑战性染色体演化范式：以脊椎动物为重点的实证与理论洞察（第二部分）’专题议题的组成部分。