Near telomere-to-telomere nuclear phased chromosomes of the dikaryotic wheat fungus Rhizoctonia cerealis
Near telomere-to-telomere nuclear phased chromosomes of the dikaryotic wheat fungus Rhizoctonia cerealis
Abstract Rhizoctonia cerealis (Rce), which causes sharp eyespot, is one of the most destructive wheat pathogens. However, the genetic and molecular virulence mechanisms of Rce have not been elucidated. As a dikaryotic organism, the haplotype phasing of this fungus has not been completed so far. We applied a haplotype phasing algorithm to generate a high-quality near telomere-to-telomere nuclear-phased genome sequence of Rce strain R0301. Sixteen pairs of chromosomes were assigned to the A and B genomes with a total size of 83 Mb. Based on a dual-time course RNA-seq, 25308 genes were predicted. Genes for steroid biosynthesis and starch and sucrose metabolism were significantly enriched, together with many genes encoding carbohydrate-active enzymes (CAZymes) and secreted effector proteins, which should be involved in infection of wheat plants. Population genomic analysis of 31 isolates collected in China during the last forty years suggests that this population has not undergone substantial differentiation over time. ImportanceThe finished genome reference is the basis of revealing pathogens’ biology base. Many efforts have been made to produce the chromosome-scale assembly of fungi. However, the reference of many pathogenic fungi is highly fragmented, which prevents the analysis of genome structure variation, evolution and import pathogenicity genes. Here, we assembly the only chromosome-scale haplotype-phased reference of dikaryotic fungus so far. This assembly achieves the gold standard based on many evaluation software, which indicates that the pipeline developed in this study can be applied to assemble references for other dikaryotic organisms. This work can also promote the research on the globe’s destructive wheat pathogens, sharp eyespot, caused by R. cerealis.
Yu Yunxin、Li Xiang、Liu Jiajie、Yuan Fengping、Zeng Qingdong、Cao Wenjin、Figueroa Melania、Qin Guowei、Chen Huaigu、Dodds Peter N.、Kang Zhensheng、Liu Shengjie、Zhou Yan、Wang Changfa、Wang Xiaoting、Wu Jianhui、Mu Zhiying、Xu Haibin、Luo Yuming、Huang Lin、Liu Huiquan、Li Wei、Wang Qinhu、Han Dejun、Yang Liming
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodNanjing Hong-Yuan Biotechnology Company LimitedCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterDepartment of Agronomy, Iowa State UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterJiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, School of Life Sciences, Huaiyin Normal UniversityCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityJiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, School of Life Sciences, Huaiyin Normal UniversityCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterInstitute of Plant Protection, Jiangsu Academy of Agricultural SciencesState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterState Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University/Yangling Seed Industry Innovation CenterCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University
植物保护遗传学微生物学
telomere-to-telomereassemblyhaplotype-phaseddikaryoticgenome
Yu Yunxin,Li Xiang,Liu Jiajie,Yuan Fengping,Zeng Qingdong,Cao Wenjin,Figueroa Melania,Qin Guowei,Chen Huaigu,Dodds Peter N.,Kang Zhensheng,Liu Shengjie,Zhou Yan,Wang Changfa,Wang Xiaoting,Wu Jianhui,Mu Zhiying,Xu Haibin,Luo Yuming,Huang Lin,Liu Huiquan,Li Wei,Wang Qinhu,Han Dejun,Yang Liming.Near telomere-to-telomere nuclear phased chromosomes of the dikaryotic wheat fungus Rhizoctonia cerealis[EB/OL].(2025-03-28)[2025-05-16].https://www.biorxiv.org/content/10.1101/2022.03.18.484966.点此复制
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