Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species.
Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species.
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基因获得和丢失的独特模式：三种茄科作物物种 NBS 编码基因的不同进化模式。
DOI：
10.1534/g3.117.040485
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发表时间：
2017-05-05
期刊：
影响因子：
--
通讯作者：
Hang YY
中科院分区：
文献类型：
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作者：
Qian LH;Zhou GC;Sun XQ;Lei Z;Zhang YM;Xue JY;Hang YY
编码核苷酸结合位点(NBS)的抗性基因在植物整个生活史中对各种病原菌的防御起着关键作用。然而，对茄科植物间NBS编码基因进化模式的系统评价和确定的比较分析还很少见。本研究从马铃薯、番茄和辣椒的基因组中分别鉴定出447个、255个和306个NBS编码基因。这些基因通常在染色体上以串联排列的形式聚集，很少以单个体的形式存在。系统发育分析表明，TnLS(TIR-NBS-LRR)、CNLS(CC-NBS-LRR)和RNLS(RPW8-NBS-LRR)三个亚类各形成一个单系统支系，并通过独特的外显子/内含子结构和氨基酸基序加以区分。通过系统发育关系的比较，我们推测马铃薯、番茄和辣椒基因组中的NBS编码基因来源于150个CNL、22个TNL和4个RNL祖先基因，并在物种形成后经历了独立的基因丢失和重复事件。因此，编码NBS的基因在三个茄科物种中表现出多样化和动态的进化模式，导致了今天观察到的不同的基因数量。土豆呈现出“一致膨胀”的格局，番茄呈现出“先膨胀后收缩”的格局，辣椒呈现出“收缩”的格局。CNL在共同祖先中的早期扩展导致了这一亚类在基因数量上的优势。然而，由于其特定的功能，RNL的拷贝数仍然很低。在茄科NBS编码基因的进化过程中，物种特有的串联复制对基因扩展的贡献最大。
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.