Suzhou Polytechnic Institute of Agriculture, 215008, China.
Research Center of Plant Diversity and Systematic Evolution, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
G3 (Bethesda). 2017 May 5;7(5):1577-1585. doi: 10.1534/g3.117.040485.
Plant resistance conferred by nucleotide binding site (NBS)-encoding resistance genes plays a key role in the defense against various pathogens throughout the entire plant life cycle. However, comparative analyses for the systematic evaluation and determination of the evolutionary modes of NBS-encoding genes among Solanaceae species are rare. In this study, 447, 255, and 306 NBS-encoding genes were identified from the genomes of potato, tomato, and pepper, respectively. These genes usually clustered as tandem arrays on chromosomes; few existed as singletons. Phylogenetic analysis indicated that three subclasses [TNLs (TIR-NBS-LRR), CNLs (CC-NBS-LRR), and RNLs (RPW8-NBS-LRR)] each formed a monophyletic clade and were distinguished by unique exon/intron structures and amino acid motif sequences. By comparing phylogenetic and systematic relationships, we inferred that the NBS-encoding genes in the present genomes of potato, tomato, and pepper were derived from 150 CNL, 22 TNL, and 4 RNL ancestral genes, and underwent independent gene loss and duplication events after speciation. The NBS-encoding genes therefore exhibit diverse and dynamic evolutionary patterns in the three Solanaceae species, giving rise to the discrepant gene numbers observed today. Potato shows a "consistent expansion" pattern, tomato exhibits a pattern of "first expansion and then contraction," and pepper presents a "shrinking" pattern. The earlier expansion of CNLs in the common ancestor led to the dominance of this subclass in gene numbers. However, RNLs remained at low copy numbers due to their specific functions. Along the evolutionary process of NBS-encoding genes in Solanaceae, species-specific tandem duplications contributed the most to gene expansions.
植物对各种病原体的抗性是由核苷酸结合位点（NBS）编码的抗性基因决定的，这些基因在整个植物生命周期的防御中起着关键作用。然而，对茄科物种中 NBS 编码基因的系统评价和进化模式的比较分析很少。在这项研究中，分别从马铃薯、番茄和辣椒的基因组中鉴定出 447、255 和 306 个 NBS 编码基因。这些基因通常在染色体上呈串联排列；很少作为单体存在。系统发育分析表明，三个亚类[TNLs（TIR-NBS-LRR）、CNLs（CC-NBS-LRR）和 RNLs（RPW8-NBS-LRR）]分别形成单系群，并通过独特的外显子/内含子结构和氨基酸基序序列来区分。通过比较系统发育和系统发育关系，我们推断马铃薯、番茄和辣椒的现有基因组中的 NBS 编码基因来源于 150 个 CNL、22 个 TNL 和 4 个 RNL 祖先基因，在物种形成后经历了独立的基因丢失和重复事件。因此，NBS 编码基因在茄科三个物种中表现出多样化和动态的进化模式，导致今天观察到的基因数量存在差异。马铃薯表现出“一致扩张”模式，番茄表现出“先扩张后收缩”模式，辣椒呈现“收缩”模式。CNLs 在共同祖先中的早期扩张导致该亚类在基因数量上占主导地位。然而，由于其特定的功能，RNLs 的拷贝数仍然较低。随着茄科 NBS 编码基因的进化过程，物种特异性串联重复对基因扩张的贡献最大。
