Feng Bo, Li Yonglin, Liu Hongyue, Steenwyk Jacob L, David Kyle T, Tian Xiaolin, Xu Biyang, Gonçalves Carla, Opulente Dana A, LaBella Abigail L, Harrison Marie-Claire, Wolters John F, Shao Shengyuan, Chen Zhaohao, Fisher Kaitlin J, Groenewald Marizeth, Hittinger Chris Todd, Shen Xing-Xing, Rokas Antonis, Zhou Xiaofan, Li Yuanning
Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China.
Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China.
bioRxiv. 2024 Jun 6:2024.06.05.597512. doi: 10.1101/2024.06.05.597512.
Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1,154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family and genome evolution are distinct from plants, animals, and filamentous ascomycetes and are characterized by small genome sizes and smaller gene numbers but larger gene family sizes. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses-commensurate with a narrowing of metabolic niche breadth-but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.
基因的获得与丢失是基因组进化的主要驱动力；对其进行精确表征有助于深入了解主要谱系的起源和多样化。在此，我们研究了医学和技术上重要的酵母亚门酵母菌纲几乎所有已知物种的1154个基因组的基因家族进化。我们发现酵母基因家族和基因组进化不同于植物、动物和丝状子囊菌，其特点是基因组较小、基因数量较少，但基因家族规模较大。酵母中进化较快的谱系（FELs）经历了显著更高的基因丢失率——这与代谢生态位宽度的变窄相一致——但比进化较慢的姐妹谱系（SELs）具有更高的物种形成率。最常丢失的基因家族是那些参与mRNA剪接、碳水化合物代谢和细胞分裂的基因家族，可能与内含子丢失、代谢宽度和非经典细胞周期过程有关。我们的研究结果突出了基因家族收缩在酵母代谢、基因组功能和物种形成进化中的重要作用，并表明基因家族进化轨迹在主要真核谱系中存在显著差异。
