Genome sequencing and comparative genomic analysis of highly and weakly aggressive strains of Sclerotium rolfsii, the causal agent of peanut stem rot
Liying Yan,
Zhihui Wang,
Wanduo Song,
Pengmin Fan,
Yanping Kang,
Yong Lei,
Liyun Wan,
Dongxin Huai,
Yuning Chen,
Xin Wang,
Hari Sudini,
Boshou Liao
Affiliations
Liying Yan
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Zhihui Wang
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Wanduo Song
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Pengmin Fan
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Yanping Kang
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Yong Lei
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Liyun Wan
College of Agronomy, Jiangxi Agricultural University
Dongxin Huai
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Yuning Chen
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Xin Wang
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Hari Sudini
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Boshou Liao
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, P.R. China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences
Abstract Background Stem rot caused by Sclerotium rolfsii is a very important soil-borne disease of peanut. S. rolfsii is a necrotrophic plant pathogenic fungus with an extensive host range and worldwide distribution. It can infect peanut stems, roots, pegs and pods, leading to varied yield losses. S. rolfsii strains GP3 and ZY collected from peanut in different provinces of China exhibited a significant difference in aggressiveness on peanut plants by artificial inoculation test. In this study, de-novo genome sequencing of these two distinct strains was performed aiming to reveal the genomic basis of difference in aggressiveness. Results Scleotium rolfsii strains GP3 and ZY, with weak and high aggressiveness on peanut plants, exhibited similar growth rate and oxalic acid production in laboratory. The genomes of S. rolfsii strains GP3 and ZY were sequenced by Pacbio long read technology and exhibited 70.51 Mb and 70.61 Mb, with contigs of 27 and 23, and encoded 17,097 and 16,743 gene models, respectively. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires, which might be associated with aggressiveness, differed between GP3 and ZY. There were 58 and 45 unique pathogen-host interaction (PHI) genes in GP3 and ZY, respectively. The ZY strain had more carbohydrate-active enzymes (CAZymes) in its secretome than GP3, especially in the glycoside hydrolase family (GH), the carbohydrate esterase family (CBM), and the polysaccharide lyase family (PL). GP3 and ZY also had different effector candidates and putative secondary metabolite synthetic gene clusters. These results indicated that differences in PHI, secreted CAZymes, effectors and secondary metabolites may play important roles in aggressive difference between these two strains. Conclusions The data provided a further understanding of the S. rolfsii genome. Genomic comparison provided clues to the difference in aggressiveness of S. rolfsii strains.
