Yang Naibo, Ma Guoping, Chen Kenxi, Wu Xuehong
College of Plant Protection, Department of Plant Pathology, China Agricultural University, Beijing, China.
Front Microbiol. 2018 Dec 3;9:2904. doi: 10.3389/fmicb.2018.02904. eCollection 2018.
A total of 32,284 unigenes were obtained from the transcriptome of , a pathogenic fungus causing foliar disease in tomato, using next-generation sequencing (NGS) technology. In total, 24,670 unigenes were annotated using five databases, including NCBI non-redundant protein, Swiss-Prot, euKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and the Gene Ontology. A total of 1,140 simple sequence repeats were also identified for use as molecular markers. Sixteen of the simple sequence repeat loci were selected to study the population structure of . A population genetic analysis of 191 isolates, sampled from four geographic regions in China, indicated that had a high level of genetic diversity, and that the selected simple sequence repeat markers could reliably capture the genetic variation. The null hypothesis of random mating was rejected for all four geographic regions in China. Isolation by distance was observed for the entire data set, but not within clusters, which is indicative of barriers to gene flow among geographic regions. The analyses of Bayesian and principal coordinates, however, did not separate four geographic regions into four separate genetic clusters. The different levels of historical migration rates suggest that isolation by distance did not represent a major biological obstacle to the spread of . The potential epidemic spread of in China may occur through the transport of plant products or other factors. The presented results provide a basis for a comprehensive understanding of the population genetics of in China.
利用新一代测序（NGS）技术，从引起番茄叶部病害的致病真菌的转录组中总共获得了32284个单基因。总共使用包括NCBI非冗余蛋白质、Swiss-Prot、真核直系同源组、京都基因与基因组百科全书以及基因本体论在内的五个数据库对24670个单基因进行了注释。还总共鉴定出1140个简单序列重复序列用作分子标记。选择了16个简单序列重复位点来研究该真菌的群体结构。对从中国四个地理区域采集的191个该真菌分离株进行的群体遗传分析表明，该真菌具有高度的遗传多样性，并且所选的简单序列重复标记能够可靠地捕获遗传变异。在中国所有四个地理区域中，随机交配的零假设均被拒绝。在整个数据集中观察到了距离隔离，但在聚类内部未观察到，这表明地理区域之间存在基因流动障碍。然而，贝叶斯分析和主坐标分析并未将四个地理区域分为四个单独的遗传簇。不同水平的历史迁移率表明，距离隔离并不代表该真菌传播的主要生物学障碍。该真菌在中国的潜在流行传播可能通过植物产品运输或其他因素发生。所呈现的结果为全面了解中国该真菌的群体遗传学提供了依据。
