Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum
Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum
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DOI：
10.1016/j.cub.2022.10.025
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发表时间：
2022-12-19
期刊：
影响因子：
9.2
通讯作者：
Rokas, Antonis
中科院分区：
文献类型：
--
作者：
Li, Yuanning;Liu, Hongyue;Rokas, Antonis
研究同源基因序列和排列的变化是理解真核生物基因组进化机制的关键。以前对真核生物基因组的比较显示，在数亿年前分化的物种(例如脊椎动物、1-3种双边动物、4、5和丝状真菌6)之间存在相当大的保守性。然而，对基因组组织如何在真核生物主要谱系内部和之间进化的了解仍然不够深入。我们分析了120个具有代表性的芽生酵母物种(酵母菌亚门)的高质量基因组，研究了它们的基因组组织是如何进化的，并将其与动植物基因组组织的进化进行了比较。7我们发现，大联体(同源染色体的保存)和微联体(局部基因内容和顺序的保存)的衰退都与芽殖酵母主要分支之间的进化差异密切相关。然而，尽管大联体的衰退非常快，但在-1亿年内，许多基因的微联体--特别是代谢簇中的基因(例如，在GAL基因簇8中)--在主要支系和亚门中都被保守得更深。我们进一步发现，当比较进化分化时间相似的基因组时，芽殖酵母的大共性保守性低于动物和丝状真菌，但高于被子植物。相比之下，萌芽酵母的微结合保守性水平与哺乳动物相当，而被子植物的保守性很低。我们的结果为整个真核生物亚门的基因和基因组组织进化的节奏和模式提供了新的见解。
Examination of the changes in order and arrangement of homologous genes is key for understanding the mechanisms of genome evolution in eukaryotes. Previous comparisons between eukaryotic genomes have revealed considerable conservation across species that diverged hundreds of millions of years ago (e.g., vertebrates,1-3 bilaterian animals,4,5 and filamentous fungi6). However, understanding how genome organization evolves within and between eukaryotic major lineages remains underexplored. We analyzed high quality genomes of 120 representative budding yeast species (subphylum Saccharomycotina) spanning-400 million years of eukaryotic evolution to examine how their genome organization evolved and to compare it with the evolution of animal and plant genome organization.7 We found that the decay of both macrosynteny (the conservation of homologous chromosomes) and microsynteny (the conservation of local gene content and order) was strongly associated with evolutionary divergence across budding yeast major clades. However, although macrosynteny decayed very fast, within-100 million years, the microsynteny of many genes-especially genes in metabolic clusters (e.g., in the GAL gene cluster8)-was much more deeply conserved both within major clades and across the subphylum. We further found that when genomes with similar evolutionary divergence times were compared, budding yeasts had lower macrosynteny conservation than animals and filamentous fungi but higher conservation than angiosperms. In contrast, budding yeasts had levels of microsynteny conservation on par with mammals, whereas angiosperms exhibited very low conservation. Our results provide new insight into the tempo and mode of the evolution of gene and genome organization across an entire eukaryotic subphylum.