Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Genome Res. 2023 Oct;33(10):1673-1689. doi: 10.1101/gr.277784.123. Epub 2023 Oct 26.
Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.
超保守元件（UCEs）是进化上相距较远的物种基因组中最保守的区域，被认为发挥着关键的生物学功能。然而，一些 UCEs 在特定谱系中快速进化，它们是否促进了适应性进化仍然存在争议。在这里，我们使用增加了具有高分类覆盖度的测序基因组数量，分别从 95 种哺乳动物和 94 种鸟类基因组中鉴定出了 2191 个哺乳动物 UCEs 和 5938 个鸟类 UCEs。我们的结果表明，这些 UCEs受到功能约束，其相邻基因在组织中广泛表达，表达多样性较低。哺乳动物和鸟类 UCEs 的功能富集显示出不同的趋势，表明 UCEs 可能有助于分类群的适应性进化。关注谱系特异性加速进化，我们发现 9 种哺乳动物和 10 种鸟类测试谱系中快速进化的 UCEs比例从 0.19%到 13.2%不等。值得注意的是，高达 62.1%的测试谱系中快速进化的 UCEs更有可能是由 GC 偏向性基因转换（gBGC）引起的。一个单一的鹿科特异性 gBGC 区域包含了 uc.359 等位基因，显著改变了大鼠大脑中 和其他神经相关基因的表达。结合 eutherians 中古老 gBGC 诱导的快速进化的 UCEs 的改变的调节活性，我们的结果提供了证据，表明 gBGC 与选择之间的协同作用塑造了谱系特异性的替代模式，即使在最受约束的调节元件中也是如此。总之，我们的结果表明，gBGC 在促进 UCEs 的谱系特异性加速进化中发挥了重要作用，并进一步支持了多种进化力量塑造适应性进化的观点。
