Liu Zhenyu, Bos Jorunn I B, Armstrong Miles, Whisson Stephen C, da Cunha Luis, Torto-Alalibo Trudy, Win Joe, Avrova Anna O, Wright Frank, Birch Paul R J, Kamoun Sophien
Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio, USA.
Mol Biol Evol. 2005 Mar;22(3):659-72. doi: 10.1093/molbev/msi049. Epub 2004 Nov 17.
Phytophthora infestans, the organism responsible for the Irish famine, causes late blight, a re-emerging disease of potato and tomato. Little is known about the molecular evolution of P. infestans genes. To identify candidate effector genes (virulence or avirulence genes) that may have co-evolved with the host, we mined expressed sequence tag (EST) data from infection stages of P. infestans for secreted and potentially polymorphic genes. This led to the identification of scr74, a gene that encodes a predicted 74-amino acid secreted cysteine-rich protein with similarity to the Phytophthora cactorum phytotoxin PcF. The expression of scr74 was upregulated approximately 60-fold 2 to 4 days after inoculation of tomato and was also significantly induced during early stages of colonization of potato. The scr74 gene was found to belong to a highly polymorphic gene family within P. infestans with 21 different sequences identified. Using the approximate and maximum likelihood (ML) methods, we found that diversifying selection likely caused the extensive polymorphism observed within the scr74 gene family. Pairwise comparisons of 17 scr74 sequences revealed elevated ratios of nonsynonymous to synonymous nucleotide-substitution rates, particularly in the mature region of the proteins. Using ML, all 21 polymorphic amino acid sites were identified to be under diversifying selection. Of these 21 amino acids, 19 are located in the mature protein region, suggesting that selection may have acted on the functional portions of the proteins. Further investigation of gene copy number and organization revealed that the scr74 gene family comprises at least three copies located in a region of no more than 300 kb of the P. infestans genome. We found evidence that recombination contributed to sequence divergence within at least one gene locus. These results led us to propose an evolutionary model that involves gene duplication and recombination, followed by functional divergence of scr74 genes. This study provides support for using diversifying selection as a criterion for identifying candidate effector genes from sequence databases.
致病疫霉是导致爱尔兰饥荒的病原体，它会引发马铃薯晚疫病，这种病害在马铃薯和番茄上再度出现。人们对致病疫霉基因的分子进化了解甚少。为了鉴定可能与宿主共同进化的候选效应子基因（毒力或无毒力基因），我们从致病疫霉感染阶段的表达序列标签（EST）数据中挖掘分泌型和潜在多态性基因。这使得我们鉴定出了scr74基因，该基因编码一种预测的74个氨基酸的分泌型富含半胱氨酸蛋白，与恶疫霉植物毒素PcF具有相似性。接种番茄后2至4天，scr74的表达上调了约60倍，并且在马铃薯定殖的早期阶段也被显著诱导。发现scr74基因属于致病疫霉内一个高度多态的基因家族，已鉴定出21个不同序列。使用近似法和最大似然法（ML），我们发现多样化选择可能导致了在scr74基因家族中观察到的广泛多态性。对17个scr74序列的成对比较显示，非同义核苷酸替换率与同义核苷酸替换率的比值升高，特别是在蛋白质的成熟区域。使用ML方法，确定所有21个多态性氨基酸位点都受到多样化选择。在这21个氨基酸中，有19个位于成熟蛋白区域，这表明选择可能作用于蛋白质的功能部分。对基因拷贝数和基因组织的进一步研究表明，scr74基因家族至少包含三个拷贝，位于致病疫霉基因组不超过300 kb的区域内。我们发现有证据表明重组促成了至少一个基因座内的序列分歧。这些结果使我们提出了一个进化模型，该模型涉及基因复制和重组，随后是scr74基因的功能分化。这项研究为将多样化选择作为从序列数据库中鉴定候选效应子基因的标准提供了支持。
