PDF(Pubmed)
Abstract：
Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we report a complex and previously hidden landscape of structural divergence between the genomes of Drosophila persimilis and D. pseudoobscura, two classic species in speciation research, and study the relationships among structural variants, transposable elements, and gene expression divergence. The new assemblies confirm the already known fixed inversion differences between these species. Consistent with previous studies showing higher levels of nucleotide divergence between fixed inversions relative to collinear regions of the genome, we also find a significant overrepresentation of INDELs inside the inversions. We find that transposable elements accumulate in regions with low levels of recombination, and spatial correlation analyses reveal a strong association between transposable elements and structural variants. We also report a strong association between differentially expressed (DE) genes and structural variants and an overrepresentation of DE genes inside the fixed chromosomal inversions that separate this species pair. Interestingly, species-specific structural variants are overrepresented in DE genes involved in neural development, spermatogenesis, and oocyte-to-embryo transition. Overall, our results highlight the association of transposable elements with structural variants and their importance in driving evolutionary divergence.
摘要：
结构基因组变异是表型进化的关键驱动因素。它们可以跨越数百至数百万个碱基对，因此可以影响大量的遗传元件。尽管物种内部和物种之间的结构变化非常普遍，其特征取决于基因组组装的质量和重复元件的比例。使用新的高质量基因组组装，我们报告了果蝇和假果蝇基因组之间结构差异的复杂且先前隐藏的景观。物种形成研究中的两个经典物种，并研究结构变体之间的关系，转座因子,和基因表达分歧。新的组件证实了这些物种之间已知的固定反转差异。与先前的研究一致，显示相对于基因组的共线区域，固定倒位之间的核苷酸差异水平更高，我们还发现倒立内部的INDEL存在明显的过多表现。我们发现转座因子在重组水平低的区域积累，和空间相关性分析揭示了转座因子和结构变体之间的强关联。我们还报告了差异表达（DE）基因与结构变体之间的强烈关联，以及将该物种对分开的固定染色体倒位内DE基因的过度表达。有趣的是,物种特异性结构变异在参与神经发育的DE基因中被过度代表，精子发生，和卵母细胞到胚胎的过渡。总的来说,我们的结果强调了转座因子与结构变异的关联及其在驱动进化差异中的重要性.
