Table_7_Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae.XLSX

Sulfolobaceae family, comprising diverse thermoacidophilic and aerobic sulfur-metabolizing Archaea from various geographical locations, offers an ideal opportunity to infer the evolutionary dynamics across the members of this family. Comparative pan-genomics coupled with evolutionary analyses has revealed asymmetric genome evolution within the Sulfolobaceae family. The trend of genome streamlining followed by periods of differential gene gains resulted in an overall genome expansion in some species of this family, whereas there was reduction in others. Among the core genes, both Sulfolobus islandicus and Saccharolobus solfataricus showed a considerable fraction of positively selected genes and also higher frequencies of gene acquisition. In contrast, Sulfolobus acidocaldarius genomes experienced substantial amount of gene loss and strong purifying selection as manifested by relatively lower genome size and higher genome conservation. Central carbohydrate metabolism and sulfur metabolism coevolved with the genome diversification pattern of this archaeal family. The autotrophic CO2 fixation with three significant positively selected enzymes from S. islandicus and S. solfataricus was found to be more imperative than heterotrophic CO2 fixation for Sulfolobaceae. Overall, our analysis provides an insight into the interplay of various genomic adaptation strategies including gene gain–loss, mutation, and selection influencing genome diversification of Sulfolobaceae at various taxonomic levels and geographical locations.

硫化叶菌科（Sulfolobaceae）包含来自不同地理区域的多样嗜热嗜酸、好氧硫代谢古菌，为解析该科类群的进化动态提供了理想研究契机。结合进化分析的比较泛基因组学研究揭示了硫化叶菌科内部存在不对称的基因组进化模式：该类群先经历基因组精简阶段，随后伴随差异化的基因获得过程，最终使得该科部分物种的基因组整体扩张，而另一些物种则出现基因组缩减。在核心基因层面，冰岛硫化叶菌（Sulfolobus islandicus）与索氏硫化叶菌（Saccharolobus solfataricus）均携带相当比例的正选择基因，同时二者的基因获取频率也更高。与之形成鲜明对比的是，嗜酸热硫化叶菌（Sulfolobus acidocaldarius）的基因组则经历了大量基因丢失事件与强烈的纯化选择，这一点从其相对较小的基因组规模与更高的基因组保守性中可见一斑。中心碳水化合物代谢与硫代谢与该古菌科的基因组分化模式协同进化。研究发现，对于硫化叶菌科而言，自养CO₂固定途径（其中冰岛硫化叶菌与索氏硫化叶菌的3种关键正选择酶参与其中）相较于异养CO₂固定途径更为关键。综上，本研究深入解析了包括基因得失、突变与选择在内的多种基因组适应策略之间的相互作用，这些策略在不同分类学层级与地理区域下共同影响了硫化叶菌科的基因组分化。