The impact of tandem duplication on gene evolution in Solanaceae species

doi:10.1016/S2095-3119(21)63698-5

摘要/Abstract

摘要：

在植物基因组进化中普遍发生的全基因组加倍 (WGD) 和串联复制 (TD) 是基因扩增和功能创新的重要形式。我们分析了三个茄科物种 (番茄、辣椒和矮牵牛) 的基因组，这些茄科物种相对于与葡萄、可可和咖啡经历了一次额外的全基因组三倍化 (WGT) 事件。我们发现没有经历过这次WGT事件的葡萄比经历过WGT事件的茄科物种保留了相对更多和更长的串联复制基因簇 (TDG)，并且发现较长TDG簇的形成往往来自于较古老的TD事件，这表明连续TD的基因（绝对剂量效应）在进化过程中长期积累。此外，茄科WGD和TD在基因保留的功能类别上表现出明显的偏向。WGD倾向于保留与生物过程有关的剂量敏感基因，包括DNA结合和转录因子活性等。TD倾向于保留参与逆境胁迫的绝对剂量基因。WGD和TD还通过基因融合和分裂为基因功能创新提供了更多途径。含有抗番茄镰刀菌枯萎病基因I3的TDG簇包含了15个串联重复基因，其中Solyc07g055560在串联重复事件后还经历了基因融合事件。这些结果为阐明TDG在适应环境变化中的新功能形成提供了依据。

Abstract: Whole genome duplication (WGD) and tandem duplication (TD) are important modes of gene amplification and functional innovation, and they are common in plant genome evolution. We analyzed the genomes of three Solanaceae species (Solanum lycopersicum, Capsicum annuum, and Petunia inflata), which share a common distant ancestor with Vitis vinifera, Theobroma cacao, and Coffea canephora but have undergone an extra whole genome triplication (WGT) event. The analysis was used to investigate the phenomenon of tandem gene evolution with (S. lycopersicum) or without WGT (V. vinifera). Among the tandem gene arrays in these genomes, we found that V. vinifera, which has not experienced the WGT event, retained relatively more and larger tandem duplicated gene (TDG) clusters than the Solanaceae species that experienced the WGT event. Larger TDG clusters tend to be derived from older TD events, so this indicates that continuous TDGs (absolute dosage) accumulated during long-term evolution. In addition, WGD and TD show a significant bias in the functional categories of the genes retained. WGD tends to retain dose-sensitive genes related to biological processes, including DNA-binding and transcription factor activity, while TD tends to retain genes involved in stress resistance. WGD and TD also provide more possibilities for gene functional innovation through gene fusion and fission. The TDG cluster containing the tomato fusarium wilt resistance gene I3 contains 15 genes, and one of these genes, Solyc07g055560, has undergone a fusion event after the duplication events. These data provide evidence that helps explain the new functionalization of TDGs in adapting to environmental changes.

Key words: tandem duplication , whole genome duplication , Solanaceae species , gene retention , gene fusion

. [J]. Journal of Integrative Agriculture, 2022, 21(4): 1004-1014.

HUANG Yi-le, ZHANG Ling-kui, ZHANG Kang, CHEN Shu-min, HU Jian-bin, CHENG Feng. The impact of tandem duplication on gene evolution in Solanaceae species[J]. Journal of Integrative Agriculture, 2022, 21(4): 1004-1014.

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