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.
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。