Abstract

Whole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here, we present Synteny-guided CORrection of Paralogies and Orthologies (SCORPiOs), a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-My-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.

中文翻译：

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同步引导的基因树解析阐明了整个基因组重复的功能影响。

摘要

全基因组重复（WGD）对物种的进化具有重大影响，因为它们产生新的基因拷贝，从而极大地促进了适应性，分离性，表型的稳健性和可进化性。它们导致大的，复杂的基因家族，在后代物种中经常发生基因丢失，而基于序列的系统发育方法无法准确重建。结果，很难在WGD下降的物种中可靠地鉴定直系同源物和旁系同源物，这阻碍了对WGDs功能后果的探索。在这里，我们目前提出的旁系同源和正交学（SCORPiOs）同步引导校正，一种在已知WGD事件背景下重建基因系统发育的新颖方法。WGD会生成大量重复的同音区域，SCORPiOs系统地利用该序列作为序列进化的补充，以推断基因的进化历史。我们在硬骨鱼的起源处将SCORPiOs应用于320-My-old WGD。我们发现，在Ensembl数据库（3,394）中，几乎有四分之一的硬骨鱼基因系统发育与其同义语境不一致。对于这些基因家族中的70％（2,387），我们能够提出与分子取代距离和局部同义信息一致的改良的系统树。我们显示，与通过最新方法产生的那些进化树相比，这些由同性指导的系统发育树与物种树，序列进化和预期的表达保守模式更加一致。最后，