Supplementary Files S3 It contains the annotation of full-length ERVs made by LTRharvest/LTRdigest. 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)’.

学界已广泛观测到一类模式：限性染色体（Y染色体与W染色体）的非重组区域相较于基因组其余区域会积累更多重复序列，即便在全基因组重复序列含量较低的鸟类等物种中亦是如此。本研究针对性染色体高度异形的鸟类展开分析，结果显示：其W染色体的转座因子（transposable element, TE）密度超过55%，而全基因组转座因子密度不足10%；且该染色体承载了全基因组超过半数的完整（即具备潜在活性）内源性逆转录病毒（endogenous retroviruses, ERVs）。本研究借助RNA测序（RNA-seq）与蛋白质质谱数据，成功检测到雌性特异性内源性逆转录病毒的表达特征。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，这大概率会引发雌性偏向的突变负荷，进而影响雌性生理机能，其效应类似于果蝇（Drosophila）中的‘毒性Y’效应。此外，霍尔丹法则（Haldane's rule）预测：异配性别（heterogametic sex）的杂交个体生育力会出现下降。我们认为，W染色体上活性内源性逆转录病毒的过量富集，可作为霍尔丹法则的额外解释变量；该机制可通过杂交个体中转座因子与阻遏蛋白的不匹配，引发物种间的遗传不相容性（genetic incompatibilities）。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，远超出性别决定与基因剂量调控的范畴。本文属于主题专刊《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）》的稿件。