Supplementary Files S7 De-novo repeat libraries: Excel factsheet with description and fasta files. 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)’.

目前学界已广泛观测到一类共性演化规律：相较于基因组其余区域，性限制染色体（sex-limited chromosomes）的非重组区域（non-recombining regions，即Y、W染色体）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类群中亦是如此。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%；同时该染色体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）。本研究借助RNA测序（RNA-seq）与蛋白质质谱（protein mass spectrometry）数据，成功检测到雌性特异性ERV表达的特征信号。据此我们提出假说：鸟类W染色体可作为活性ERVs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，其机制与果蝇（Drosophila）中的"毒性Y效应"（toxic-Y effect）类似。此外，霍尔丹法则（Haldane's rule）预言，杂交子代的异配性别个体生育力会出现下降。我们提出，W染色体上活性ERVs的富集程度远高于基因组其余区域，这可作为解释霍尔丹法则的额外变量：杂交后代中转座因子与阻遏蛋白的错配，会引发物种间的遗传不相容问题。综上，本研究结果表明，雌性特异性W染色体的序列组成，其影响远不止于性别决定与基因剂量调控。本文隶属于专题刊"挑战性染色体演化范式：以脊椎动物为核心的实证与理论进展（第二部分）"。