Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies
Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies
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DOI：
10.1007/s00239-001-0057-2
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发表时间：
2002-04-01
影响因子：
3.9
通讯作者：
Young, ND
中科院分区：
文献类型：
--
作者：
Cannon, SB;Zhu, HY;Young, ND
对9个科30个属的NBS-LRR（nucleotide binding site-leucine-rich repeat）抗性基因同源物（RGH）进行了系统发育分析。分析了800多个NBS-LRR RGH，主要来自豆科、豆科、禾本科和茄科物种，但也来自其他被子植物和裸子植物科的代表。简约，最大似然，距离的方法被用来对这些RGH相对于以前观察到的基因亚家族，以及在更密切相关的序列进化枝。使用250个PAM单位（每100个残基的点接受突变）的距离截止值的PCR序列鉴定了至少5个古老的序列进化枝，其代表来自几个植物家族：先前观察到的TIR基因亚家族和非TIR基因亚家族内最少4个深分裂。非TIR亚家族的深度分裂也反映在不同物种的氨基酸取代率的比较和拟南芥中非同义与同义核苷酸取代率的比值（K-A/K-S值）中。TIR序列中的K-A/K-S值低于非TIR序列，表明TIR亚家族中存在更大的功能限制。至少有三个确定的古代分支出现之前的被子植物裸子植物辐射。单子叶植物序列是不存在的TIR亚科，在以前的研究中观察到的。在这两个亚科中，进化枝的序列分开约150 PAM单位的家庭，但不是属特异性的，提供了一个粗略的衡量这些进化枝内的第一次多样化事件的最低日期。在任何一个分支，特定的类群可能会显着过度或代表性不足，这表明在特定类群的某些RGH类型的优先扩展或损失，并表明没有一个物种将提供其他类群的所有主要序列类型的模型。
Phylogenetic relationships among the NBS-LRR (nucleotide binding site-leucine-rich repeat) resistance gene homologues (RGHs) from 30 genera and nine families were evaluated relative to phylogenies for these taxa. More than 800 NBS-LRR RGHs were analyzed, primarily from Fabaceae, Brassicaceae, Poaceae, and Solanaceae species, but also from representatives of other angiosperm and gymnosperm families. Parsimony, maximum likelihood, and distance methods were used to classify these RGHs relative to previously observed gene subfamilies as well as within more closely related sequence clades. Grouping sequences using a distance cutoff of 250 PAM units (point accepted mutations per 100 residues) identified at least five ancient sequence clades with representatives from several plant families: the previously observed TIR gene subfamily and a minimum of four deep splits within the non-TIR gene subfamily. The deep splits in the non-TIR subfamily are also reflected in comparisons of amino acid substitution rates in various species and in ratios of nonsynonymous-to-synonymous nucleotide substitution rates (K-A/K-S values) in Arabidopsis thaliana. Lower K-A/K-S values in the TIR than the non-TIR sequences suggest greater functional constraints in the TIR subfamily. At least three of the five identified ancient clades appear to predate the angiosperm-gymnosperm radiation. Monocot sequences are absent from the TIR subfamily, as observed in previous studies. In both subfamilies, clades with sequences separated by approximately 150 PAM units are family but not genus specific, providing a rough measure of minimum dates for the first diversification event within these clades. Within any one clade, particular taxa may be dramatically over- or underrepresented, suggesting preferential expansions or losses of certain RGH types within particular taxa and suggesting that no one species will provide models for all major sequence types in other taxa.