The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA;
Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA.
Genome Res. 2023 Apr;33(4):557-571. doi: 10.1101/gr.277434.122. Epub 2023 May 5.
Because of diverged adaptative phenotypes, fish species of the genus have contributed to a wide range of research for a century. Existing 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 species, namely, , , and Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the 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.
由于适应不同环境的表型差异，属的鱼类物种在一个世纪以来为广泛的研究做出了贡献。现有的基因组组装水平还没有达到染色体级别，并且容易出现序列缺口，从而阻碍了种内和种间差异的进化、比较和转化医学研究的进展。在此，我们为三个远缘相关的物种组装了高质量的染色体水平基因组组装体，分别是 、 、 和 。我们的总体目标是精确评估进化枝中的微进化过程，以确定导致物种分化的分子事件，并深入了解导致疾病的遗传不相容性。特别是，我们测量了三个物种之间的种内和种间分歧，并评估了种间正反交杂种的基因表达失调情况。我们发现了与胎生（一种特殊的繁殖方式）相关的扩展基因家族和正选择基因。我们还发现，正选择基因家族在非多态转座元件中显著富集，这表明这些非多态转座元件的扩散伴随着基因的进化，可能通过整合新的调控元件来支持 Britten-Davidson 假说。我们描述了种间多态性、结构变异和多态转座元件插入，并评估了它们与种间杂交诱导的基因表达失调之间的关联，这些基因表达失调与人类特定疾病状态有关。
