基因组组合的染色体水平草稿Hypomesus nipponensis揭示了可转移的元素扩张,重塑了基因组结构
Chenzhao Zhu1,2, Youyi Kuang2, Zhe Li2
1College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
Frontiers in genetics
|May 19, 2025
概括
对商业重要鱼类Hypomesus nipponensis的新染色体层次基因组组件揭示了其进化历史和奥斯梅里formes序列中的基因组多样性的洞察力.
科学领域:
- 基因组学就是基因组学.
- 进化生物学 进化生物学
- 水产养殖是水产养殖的一种方式.
背景情况:
- 鱼 (Hypomesus nipponensis) 是一个商业上有价值的鱼,属于鱼类 (Osmeriformes) 类,原产于东北亚,并被广泛用于水产养殖.
- 之前对H. nipponensis的基因组研究受到组件连续性和完整性的限制.
研究的目的:
- 为了生成一个高质量的,染色体水平的基因组组合Hypomesus nipponensis.
- 为了研究H. nipponensis在Osmeridae家族中的进化史和基因组多样性.
- 为基础生物研究和水产养殖应用提供基因组资源.
主要方法:
- 使用PacBio HiFi和连续长读 (CLR) 测序进行De novo基因组组.
- 使用相关物种的合成信息来改进组装,以实现染色体水平的连续性.
- 与Osmerus eperlanus和Hypomesus transpacificus进行基因组比较分析.
主要成果:
- 一个507.8 Mb的染色体层次基因组组件,一个20 Mb的N50支架,比以前的组件更加连续和完整.
- 鉴定出高比例的并列重复,并近期显著扩展了转位子和相似基因家族.
- 估计H. nipponensis,O. eperlanus和H. transpacificus之间的分歧时间大约在2410万年前,有染色体重组的证据.
- 发现O. eperlanus中的存在/缺席变异 (PAV) 主要与免疫反应基因有关.
结论:
- 提升的染色体级基因组组合H. nipponensis为了解其进化轨迹和基因组特征提供了宝贵的资源.
- 这些发现揭示了H. nipponensis进化的基因组基础,包括重复元素动态和基因家族扩展.
- 比较基因组学揭示了免疫相关基因在鱼类物种分歧中的潜在作用.
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