Li Shaojian, Wang Zhenyu, Gao Meng, Li Tong, Cui Xiaowei, Zu Junhuai, Sang Suling, Fan Wanwan, Zhang Haiyan
Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China.
Biology (Basel). 2023 Mar 21;12(3):476. doi: 10.3390/biology12030476.
is one of the most important fungal pathogens, causing foliar disease and leading to severe yield losses of peanuts ( L.) in China. Two main lesion phenotypes of peanut web blotch have been identified as reticulation type (R type) and blotch type (B type). As no satisfactory reference genome is available, the genomic variations and pathogenicity factors of remain to be revealed. In the present study, we collected 41 isolates from 26 geographic locations across China (33 for R type and 8 for B type). The chromosome-scale genome of the most virulent isolate (YY187) was assembled as a reference using PacBio and Hi-C technologies. In addition, we re-sequenced 40 isolates from different sampling sites. Genome-wide alignments showed high similarity among the genomic sequences from the 40 isolates, with an average mapping rate of 97.38%. An average of 3242 SNPs and 315 InDels were identified in the genomic variation analysis, which revealed an intraspecific polymorphism in . The comparative analysis of the most and least virulent isolates generated an integrated gene set containing 512 differential genes. Moreover, 225 genes individually or simultaneously harbored hits in CAZy-base, PHI-base, DFVF, etc. Compared with the R type reference, the differential gene sets from all B type isolates identified 13 shared genes potentially related to lesion phenotype. Our results reveal the intraspecific genomic variation of isolates and pathogenicity factors potentially related to different lesion phenotypes. This work sets a genomic foundation for understanding the mechanisms behind genomic diversity driving different pathogenic phenotypes of .
是最重要的真菌病原体之一，在中国导致花生叶部病害并造成严重产量损失。花生网斑病的两种主要病斑表型已被确定为网状型（R型）和斑点型（B型）。由于没有令人满意的参考基因组，其基因组变异和致病因素仍有待揭示。在本研究中，我们从中国26个地理位置收集了41个菌株（R型33个，B型8个）。使用PacBio和Hi-C技术组装了最具毒性的菌株（YY187）的染色体级基因组作为参考。此外，我们对来自不同采样地点的40个菌株进行了重测序。全基因组比对显示40个菌株的基因组序列之间具有高度相似性，平均映射率为97.38%。在基因组变异分析中平均鉴定出3242个单核苷酸多态性（SNP）和315个插入缺失（InDel），揭示了种内多态性。对最具毒性和毒性最小的菌株进行比较分析，生成了一个包含512个差异基因的整合基因集。此外，225个基因在碳水化合物活性酶数据库（CAZy-base）、植物致病因子数据库（PHI-base）、真菌病毒数据库（DFVF）等中单独或同时有匹配。与R型参考相比，所有B型菌株的差异基因集鉴定出13个可能与病斑表型相关的共享基因。我们的结果揭示了菌株的种内基因组变异以及与不同病斑表型潜在相关的致病因素。这项工作为理解驱动不同致病表型的基因组多样性背后的机制奠定了基因组基础。
