Abstract:
Due to the difficulty in accurately identifying structural variants (SVs) across genomes, their impact on cis-regulatory divergence of closely related species, especially fish, remains to be explored. Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes. However, the role of broad H3K4me3 domains in phenotypic divergence remains poorly understood. Siniperca chuatsi and S. scherzeri are closely related but divergent in several phenotypic traits, making them an ideal model to study cis-regulatory evolution in sister species. Here, we generated chromosome-level genomes of S. chuatsi and S. scherzeri, with assembled genome sizes of 716.35 and 740.54 Mb, respectively. The evolutionary histories of S. chuatsi and S. scherzeri were studied by inferring dynamic changes in ancestral population sizes. To explore the genetic basis of adaptation in S. chuatsi and S. scherzeri, we performed gene family expansion and contraction analysis and identified positively selected genes (PSGs). To investigate the role of SVs in cis-regulatory divergence of closely related fish species, we identified high-quality SVs as well as divergent H3K27ac and H3K4me3 domains in the genomes of S. chuatsi and S. scherzeri. Integrated analysis revealed that cis-regulatory divergence caused by SVs played an essential role in phenotypic divergence between S. chuatsi and S. scherzeri. Additionally, divergent broad H3K4me3 domains were mostly associated with cancer-related genes in S. chuatsi and S. scherzeri and contributed to their phenotypic divergence.
由于难以在基因组中全面地鉴定结构变异,我们仍然缺乏对结构变异在近缘物种,特别是鱼类近缘物种顺式调控趋异中作用的认知。近期的研究发现,宽H3K4me3峰在多个生物学过程的基因调控中起关键作用。然而,宽H3K4me3峰在物种表型趋异中的作用仍然未知。翘嘴鳜( Siniperca chuatsi)和斑鳜( Siniperca scherzeri)是一对姐妹种,但是它们在多个性状上有很大差异。这使得它们成为研究顺式调控演化的良好模型。我们构建了染色体级别的翘嘴鳜和斑鳜基因组,组装大小分别为716.35 Mb和740.54 Mb。通过推断历史种群大小,我们分析了翘嘴鳜和斑鳜的演化历史。通过基因家族扩张和收缩分析,以及鉴定正选择基因,我们解析了翘嘴鳜和斑鳜适应环境的遗传学基础。为了阐明结构变异在近缘鱼类物种顺式调控趋异中的作用,我们在翘嘴鳜和斑鳜基因组中鉴定了高质量的结构变异,以及差异H3K27ac和H3K4me3峰。联合分析发现,由结构变异引起的顺式调控趋异在翘嘴鳜和斑鳜表型趋异中起关键作用。此外,在翘嘴鳜和斑鳜中,差异宽H3K4me3峰主要与癌症相关基因相关联,并导致这两个物种的表型趋异。.