调查局部适应的大西洋鱼种群之间的结构变异,indel和单核酸多态差异化
Laurie Lecomte1,2, Mariann Árnyasi3, Anne-Laure Ferchaud1,2,4
1Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Canada.
Evolutionary applications
|March 18, 2024
概括
基因组结构变异 (SVs) 对进化至关重要,但在野生种群中很难研究. 这项研究成功地描述了大西洋鱼中的SVs,揭示了它们在当地适应中的作用和与神经发育的潜在联系.
科学领域:
- 人口基因组学 人口基因组学
- 进化生物学 进化生物学
- 遗传学 遗传学是一种遗传学.
背景情况:
- 基因组结构变异 (SVs) 是物种内部多态化和进化的关键,但在野生种群中使用短读序列检测具有挑战性.
- 大西洋鱼 (Salmo salar) 种群在生命历史和息地中表现出显著的变化,这使得它们非常适合研究适应多态.
- 在鱼类中,SVs对微小局部适应的贡献在很大程度上仍未被探索.
研究的目的:
- 为了比较分析结构变异 (SVs),单核酸多态 (SNPs) 和两个据称本地适应的大西洋鱼种群 (Romaine和Puyjalon) 的小体.
- 通过检查它们的分布和与生长,生育能力和成熟/小型化时的年龄的表型变异的关联来调查 SVs 在当地适应中的作用.
- 为了证明在野生鱼种群中大规模的SV表征的可行性.
主要方法:
- 采用混合测序方法,将短读 (16X) 和长读 (20X) 数据结合起来,以进行全面的变体发现.
- 利用基于图形的基因型识别来表征60个大西洋鱼基因组中的SVs.
- 使用冗余分析 (RDA) 进行了SV,SNP和小区域的比较分析,包括人口结构,FST和异常值检测.
主要成果:
- 确定了大量的变异:115,907个SV,8,777,832个SNP和1,089,321个小的indels,其中SV覆盖的基对比SNP要多得多.
- 在所有三种变种类型 (SVs,SNP,indels) 中观察到一致的种群结构和类似的FST模式和变种密度.
- 确定了与局部适应相关的候选变体,附近的基因为神经系统功能进行了丰富,这表明它在神经发育和生命史变异中的作用.
结论:
- 大规模的SV表征是可行的,并且对了解鱼种群基因组学非常重要.
- SVs有助于大西洋鱼的局部适应,可能通过改变神经发育等机制影响关键生命史特征.
- 这项研究为未来关于野生种群结构变化的进化影响的研究提供了基础.
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