Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns
Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns
复制标题
对被子植物核苷酸结合位点富含亮氨酸重复基因的大规模分析揭示了三个具有不同进化模式的古老分歧类
DOI：
10.1104/pp.15.01487
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发表时间：
2016-04-01
期刊：
影响因子：
7.4
通讯作者：
Chen, Jian-Qun
中科院分区：
文献类型：
--
作者：
Shao, Zhu-Qing;Xue, Jia-Yu;Chen, Jian-Qun
核苷酸结合位点富含亮氨酸重复序列(NBS-LRR)基因是最大的植物抗病基因家族(R基因)，在被子植物基因组中存在数百个拷贝。然而，NBS-LRR基因在被子植物进化过程中的扩展历史在很大程度上是未知的。通过在22个被子植物中鉴定出6000多个NBS-LRR基因并重建它们的系统发育关系，我们提出了被子植物中NBS-LRR基因进化的潜在框架。通过独特的外显子结构和DNA基序序列，区分了三个过去存在分歧的NBS-LRR类(TNLS、CNLS和RNLS)。在原始被子植物中发现了7个古老的TNL、14个CNL和2个RNL谱系，所有现在的NBS-LRR基因谱系都是从这些谱系进化而来的。在被子植物分支进化的最初1亿年中，观察到了一种逐渐扩大的模式。在此期间，TNL数量保持稳定，但最终在三个不同的被子植物谱系中被删除。我们推测，TnL和CNL基因的强烈扩张始于白垩纪-古近纪界线。由于在此期间发生了剧烈的环境变化和真菌多样性的爆炸性增长，所观察到的R基因的扩展可能反映了不同被子植物家族的趋同适应反应。在被子植物祖先中发生的一个古老的全基因组复制事件导致了两个RNL谱系，它们被保守地进化并作为防御信号转导的支架蛋白。总之，本研究构建的被子植物NBS-LRR基因进化框架可能为更好地理解被子植物NBS-LRR基因提供基础参考。
Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exonintron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.