Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species, namely, X. maculatus, X. couchianus, and X. hellerii. Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorus species and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten–Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.

中文翻译：

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多个剑尾鱼物种的高分辨率基因组为微进化、杂交不相容性和上位性提供了新的见解

由于适应性表型的差异，剑鱼属鱼类一个世纪以来为广泛的研究做出了贡献。现有的剑尾鱼基因组组装不在染色体水平上，并且容易出现序列缺口，从而阻碍了进化、比较和转化生物医学研究的种内和种间差异的进展。在此，我们为三个远缘剑龙物种（即X. maculatus、X. couchianus和X. hellerii）组装了高质量的染色体水平基因组组装。我们的总体目标是精确评估进化枝中的微进化过程，以确定导致剑尾鱼物种分化的分子事件，并加深对疾病遗传不相容性的理解。特别是，我们测量了种内和种间的差异，并评估了这三个物种之间相互种间杂交的基因表达失调。我们发现了与活体繁殖（一种特殊的繁殖方式）相关的扩大的基因家族和积极选择的基因。我们还发现，积极选择的基因家族显着富集非多态性转座元件，这表明这些非多态性转座元件的分散伴随着基因的进化，可能是通过纳入新的调控元件来支持布里顿-戴维森假说。我们表征了种间多态性、结构变异和多态性转座元件插入，并评估了它们与种间杂交诱导的与人类特定疾病状态相关的基因表达失调的关联。