College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
School of Life Science, Nanjing University, Nanjing, 210023, China.
BMC Genomics. 2021 Feb 9;22(1):112. doi: 10.1186/s12864-021-07422-7.
In plant genomes, high proportions of duplicate copies reveals that gene duplications play an important role in the evolutionary processes of plant species. A series of gene families under positive selection after recent duplication events in plant genomes indicated the evolution of duplicates driven by adaptive evolution. However, the genome-wide evolutionary features of young duplicate genes among closely related species are rarely reported.
In this study, we conducted a systematic survey of young duplicate genes at genome-wide levels among six Rosaceae species, whose whole-genome sequencing data were successively released in recent years. A total of 35,936 gene families were detected among the six species, in which 60.25% were generated by young duplications. The 21,650 young duplicate gene families could be divided into two expansion types based on their duplication patterns, species-specific and lineage-specific expansions. Our results showed the species-specific expansions advantaging over the lineage-specific expansions. In the two types of expansions, high-frequency duplicate domains exhibited functional preference in response to environmental stresses.
The functional preference of the young duplicate genes in both the expansion types showed that they were inclined to respond to abiotic or biotic stimuli. Moreover, young duplicate genes under positive selection in both species-specific and lineage-specific expansions suggested that they were generated to adapt to the environmental factors in Rosaceae species.
在植物基因组中，高比例的重复拷贝表明基因复制在植物物种的进化过程中起着重要作用。植物基因组中最近复制事件后的一系列正选择基因家族表明，重复的进化是由适应性进化驱动的。然而，很少有报道涉及密切相关物种中年轻重复基因的全基因组进化特征。
在这项研究中，我们对近年来相继完成全基因组测序的六个蔷薇科物种进行了全基因组范围内年轻重复基因的系统调查。在这六个物种中总共检测到 35936 个基因家族，其中 60.25%是由年轻复制产生的。21650 个年轻的重复基因家族可以根据其复制模式分为两种扩展类型：种内特异性扩张和谱系特异性扩张。我们的结果表明，种内特异性扩张比谱系特异性扩张更有利。在这两种扩张类型中，高频重复结构域在响应环境胁迫时表现出功能偏好。
两种扩张类型中的年轻重复基因的功能偏好表明它们倾向于响应非生物或生物刺激。此外，在种内特异性和谱系特异性扩张中受到正选择的年轻重复基因表明，它们的产生是为了适应蔷薇科物种中的环境因素。
