PDF(Pubmed)
Abstract：
BACKGROUND: White clover (Trifolium repens) is a globally important perennial forage legume. This species also serves as an eco-evolutionary model system for studying within-species chemical defense variation; it features a well-studied polymorphism for cyanogenesis (HCN release following tissue damage), with higher frequencies of cyanogenic plants favored in warmer locations worldwide. Using a newly generated haplotype-resolved genome and two other long-read assemblies, we tested the hypothesis that copy number variants (CNVs) at cyanogenesis genes play a role in the ability of white clover to rapidly adapt to local environments. We also examined questions on subgenome evolution in this recently evolved allotetraploid species and on chromosomal rearrangements in the broader IRLC legume clade.
RESULTS: Integration of PacBio HiFi, Omni-C, Illumina, and linkage map data yielded a completely de novo genome assembly for white clover (created without a priori sequence assignment to subgenomes). We find that white clover has undergone extensive transposon diversification since its origin but otherwise shows highly conserved genome organization and composition with its diploid progenitors. Unlike some other clover species, its chromosomal structure is conserved with other IRLC legumes. We further find extensive evidence of CNVs at the major cyanogenesis loci; these contribute to quantitative variation in the cyanogenic phenotype and to local adaptation across wild North American populations.
CONCLUSIONS: This work provides a case study documenting the role of CNVs in local adaptation in a plant species, and it highlights the value of pan-genome data for identifying contributions of structural variants to adaptation in nature.
RESULTS: Integration of PacBio HiFi, Omni-C, Illumina, and linkage map data yielded a completely de novo genome assembly for white clover (created without a priori sequence assignment to subgenomes). We find that white clover has undergone extensive transposon diversification since its origin but otherwise shows highly conserved genome organization and composition with its diploid progenitors. Unlike some other clover species, its chromosomal structure is conserved with other IRLC legumes. We further find extensive evidence of CNVs at the major cyanogenesis loci; these contribute to quantitative variation in the cyanogenic phenotype and to local adaptation across wild North American populations.
CONCLUSIONS: This work provides a case study documenting the role of CNVs in local adaptation in a plant species, and it highlights the value of pan-genome data for identifying contributions of structural variants to adaptation in nature.
摘要：
背景：白三叶（白三叶）是全球重要的多年生牧草豆科植物。该物种还可以作为研究物种内化学防御变异的生态进化模型系统；它具有充分研究的氰化多态性（组织损伤后HCN释放），在全球较温暖的地区，生氰植物的频率较高。使用新生成的单倍型解析基因组和另外两个长读组件，我们检验了一个假设,即氰化生基因的拷贝数变异(CNVs)在白三叶草快速适应局部环境的能力中起作用.我们还研究了这种最近进化的异源四倍体物种的亚基因组进化以及更广泛的IRLC豆科植物进化枝的染色体重排问题。
结果：PacBioHiFi的集成，Omni-C,Illumina,和连锁图谱数据产生了白三叶草的完全从头基因组组装（在没有子基因组的先验序列分配的情况下创建）。我们发现，白三叶草自起源以来经历了广泛的转座子多样化，但在其他方面，其二倍体祖细胞显示出高度保守的基因组组织和组成。与其他一些三叶草物种不同，其染色体结构与其他IRLC豆类保守。我们进一步在主要的发蓝位点发现了CNV的大量证据；这些有助于生氰表型的定量变化和北美野生种群的局部适应。
结论：这项工作提供了一个案例研究，记录了CNVs在植物物种局部适应中的作用，它强调了泛基因组数据对识别结构变异对自然界适应的贡献的价值。
结果：PacBioHiFi的集成，Omni-C,Illumina,和连锁图谱数据产生了白三叶草的完全从头基因组组装（在没有子基因组的先验序列分配的情况下创建）。我们发现，白三叶草自起源以来经历了广泛的转座子多样化，但在其他方面，其二倍体祖细胞显示出高度保守的基因组组织和组成。与其他一些三叶草物种不同，其染色体结构与其他IRLC豆类保守。我们进一步在主要的发蓝位点发现了CNV的大量证据；这些有助于生氰表型的定量变化和北美野生种群的局部适应。
结论：这项工作提供了一个案例研究，记录了CNVs在植物物种局部适应中的作用，它强调了泛基因组数据对识别结构变异对自然界适应的贡献的价值。
