Mantica Federica, Irimia Manuel
Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain.
Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
Genome Biol. 2025 Sep 4;26(1):268. doi: 10.1186/s13059-025-03699-z.
Vertebrates and insects diverged approximately 700 million years ago, and yet they retain a large core of conserved genes from their last common ancestor. These ancient genes present strong evolutionary constraints, which limit their overall sequence and expression divergence. However, these constraints can greatly vary across ancestral gene families and, in at least some cases, sequence and expression changes can have functional consequences. Importantly, overall patterns of sequence and expression divergence and their potential functional outcomes have never been explored in a genome-wide manner across large animal evolutionary distances.
We focus on approximately 7000 highly conserved genes shared between vertebrates and insects, and we investigate global patterns of molecular diversification driven by changes in sequence and gene expression. We identify molecular features generally linked to higher or lower diversification rates, together with gene groups with similar diversification profiles in both clades. Moreover, we discover that specific sets of genes underwent differential diversification during vertebrate and insect evolution, potentially contributing to the emergence of unique phenotypes in each clade.
We generate a comprehensive dataset of measures of sequence and expression divergence across vertebrates and insects, which reveals a continuous spectrum of evolutionary constraints among highly conserved genes. These constraints are normally consistent between these two clades and are associated with specific molecular features, but in some cases we also identify instances of lineage-specific diversification likely linked to functional evolution.
脊椎动物和昆虫大约在7亿年前分化，但它们仍保留了来自其最后一个共同祖先的大量核心保守基因。这些古老基因存在很强的进化限制，这限制了它们的整体序列和表达差异。然而，这些限制在祖先基因家族中差异很大，并且在至少某些情况下，序列和表达变化可能具有功能后果。重要的是，从未在全基因组范围内跨越较大的动物进化距离探索过序列和表达差异的总体模式及其潜在的功能结果。
我们聚焦于脊椎动物和昆虫之间共享的约7000个高度保守基因，并研究由序列和基因表达变化驱动的分子多样化的全局模式。我们确定了通常与较高或较低多样化率相关的分子特征，以及两个进化枝中具有相似多样化特征的基因组。此外，我们发现特定的基因集在脊椎动物和昆虫进化过程中经历了差异多样化，这可能有助于每个进化枝中独特表型的出现。
我们生成了一个关于脊椎动物和昆虫序列和表达差异测量的综合数据集，揭示了高度保守基因之间连续的进化限制谱。这些限制在这两个进化枝之间通常是一致的，并且与特定的分子特征相关，但在某些情况下，我们也发现了可能与功能进化相关的谱系特异性多样化实例。
