X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, Musca domestica. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The up-regulation of the proto-Y allele may be favored in males because of this gene’s function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.

中文翻译：

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一个非常年轻的家蝇原始Y染色体与其同源X染色体之间的基因水平而非染色体范围的差异

X和Y染色体通常来自一对同源常染色体，然后随着时间的流逝彼此分离。尽管在各个年龄的性染色体中都有Y特有的特征，但Y染色体进化的最早阶段仍然难以捉摸。特别是，我们不知道Y染色体进化的早期阶段是由单个基因的变化还是通过与X的染色体尺度差异而发生的。为解决这个问题，我们对年轻的X染色体和Pro-Y染色体之间的差异进行了量化。家蝇，家蝇。我们比较了基因型（XY）和性别反转（XX）男性之间的原型性别染色体序列和基因表达。我们发现证据证明原X和原Y基因之间的序列差异，包括具有线粒体功能的5个基因。在proto-X和proto-Y之间也有过多的基因表达差异，但是基因的数量很少。这表明单个的原始Y基因，而不是整个原始Y染色体，已经偏离了原始X。我们确定了一个编码轴突动力蛋白装配因子（在精子运动中起作用）的基因，该基因在XY雄性中的表达高于XX雄性，这是因为原Y等位基因对基因表达的贡献不成比例。由于该基因在精子发生中的功能，男性可能更倾向于原Y等位基因的上调。