Department of Biology, University of Maryland, College Park, MD, USA.
Genome Biol Evol. 2024 Mar 2;16(3). doi: 10.1093/gbe/evae047.
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.
结构基因组变异是表型进化的关键驱动因素。它们可以跨越数百到数百万个碱基对，因此可以影响大量的遗传元件。尽管结构变异在物种内和物种间相当普遍，但它的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，我们报告了在果蝇 persimilis 和 D. pseudoobscura 这两个物种分化研究中的经典物种的基因组之间存在复杂而先前隐藏的结构分化景观，并研究了结构变异、转座元件和基因表达分化之间的关系。新的组装证实了这些物种之间已经存在的固定倒位差异。与先前的研究一致，即固定倒位之间的核苷酸差异水平高于基因组的共线性区域，我们也发现了 INDEL 在倒位内的显著过表达。我们发现转座元件在重组水平低的区域积累，空间相关分析揭示了转座元件与结构变异之间的强烈关联。我们还报告了差异表达（DE）基因与结构变异之间的强烈关联，以及在分离该物种对的固定染色体倒位内 DE 基因的过表达。有趣的是，与神经发育、精子发生和卵母细胞到胚胎转变相关的 DE 基因中存在物种特异性的结构变异。总的来说，我们的结果强调了转座元件与结构变异的关联及其在驱动进化分化中的重要性。
