Pervasive purifying selection characterizes the evolution of I2 homologs
Pervasive purifying selection characterizes the evolution of I2 homologs
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DOI：
10.1094/mpmi-19-0288
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发表时间：
2006-03-01
影响因子：
3.5
通讯作者：
May, G
中科院分区：
文献类型：
--
作者：
Couch, BC;Spangler, R;May, G
本研究从马铃薯、番茄、番茄属6个物种中获得了384个与番茄抗病基因12相关的序列。demissum，番茄，茄子，辣椒和烟草。这些物种代表了茄科内从马铃薯到烟草的系统发育距离的增加。使用该基因的核苷酸结合位点（NBS）区域的序列数据，我们测试了基因家族进化的模型，并推断了作用于NBS基因区域和12个基因家族的选择模式。我们认为，12家族在茄科中已经多样化了至少1400万年，并且通过一个缓慢的出生和死亡过程进化，需要大约1200万年来使一个物种内的基因拷贝均匀化。选择分析解决了一个一般模式的强大的纯化选择作用于NBS内的各个密码子位置和NBS谱系通过时间。令人惊讶的是，我们发现9个密码子的位置受到积极的选择和6对密码子的位置表现出相关的氨基酸取代的强烈影响。进化分析作为生物信息学工具，通过在植物和果皮候选人的巨大的R基因多样性进行排序，以新的抗性特异性或确定特定的氨基酸位置重要的生化功能。12个基因的缓慢的出生和死亡进化表明，一些富含NBS-leucine repeatmediated抗性可能不会被毒力进化迅速克服，R基因的天然多样性是持久抗性的潜在有价值的来源。
We sampled 384 sequences related to the Solanum pimpinel-lifolium (=Lycopersicon pimpinellifolium) disease resistance (R) gene 12 from six species, potato, S. demissum, tomato, eggplant, pepper, and tobacco. These species represent increasing phylogenetic distance from potato to tobacco, within the family Solanaceae. Using sequence data from the nucleotide binding site (NBS) region of this gene, we tested models of gene family evolution and inferred patterns of selection acting on the NBS gene region and 12 gene family. We rind that the 12 family has diversified within the family Solanaceae for at least 14 million years and evolves through a slow birth-and-death process requiring approximately 12 million years to homogenize gene copies within a species. Analyses of selection resolved a general pattern of strong purifying selection acting on individual codon positions within the NBS and on NBS lineages through time. Surprisingly, we find nine codon positions strongly affected by positive selection and six pairs of codon positions demonstrating correlated amino acid substitutions. Evolutionary analyses serve as bioinformatic tools with which to sort through the vast R gene diversity in plants and rind candidates for new resistance specificities or to identify specific amino acid positions important for biochemical function. The slow birth-and-death evolution of 12 genes suggests that some NBS-leucine rich repeatmediated resistances may not be overcome rapidly by virulence evolution and that the natural diversity of R genes is a potentially valuable source for durable resistance.