Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
Department of Horticulture, Michigan State University, East Lansing, MI, USA.
Mol Biol Evol. 2021 Jun 25;38(7):2692-2703. doi: 10.1093/molbev/msab042.
Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only PAV and positional variation (PosV) but that diversity in CNS is nonrandom, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting roles for conserved and variable CNS in gene regulation. Additionally, our data suggests that transposable elements contribute to CNS variation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.
最近的泛基因组研究揭示了物种内很大一部分基因内容表现出存在-缺失变异（PAV）。然而，仅编码区域提供了对物种水平功能基因组序列变异的不完整评估。在泛基因组研究中，很少关注非编码调控区域，尽管这些序列直接调节基因表达和表型。为了揭示调控遗传变异，我们为来自多个不同生境的 30 个拟南芥品系生成了染色体规模的基因组组装，并对保守非编码序列（CNS）中的物种水平变异进行了特征描述。我们的分析不仅揭示了 PAV 和位置变异（PosV），而且还表明 CNS 中的多样性是非随机的，不同品系之间存在共享的变体。通过进化分析和染色质可及性数据，我们提供了进一步的证据，支持保守和可变 CNS 在基因调控中的作用。此外，我们的数据表明转座元件有助于 CNS 变异。对所有功能基因组序列的物种水平多样性进行特征描述，可能会揭示基因型和表型之间以前未知的机制联系。
