title: A host plant genome (Zizania latifolia) after a century-long endophyte infection.
abstract: Despite the importance of host-microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop 'Jiaobai' with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z. latifolia-endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant-pathogen interaction pathway in Jiaobai. These results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
authors.forename: Longbiao
authors.initials: L
authors.lastname: Guo
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Qiu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Zujing
authors.initials: Z
authors.lastname: Han
authors.affiliation: College of Life Science, China Jiliang University, Hangzhou, 310018, China.
authors.forename: Zihong
authors.initials: Z
authors.lastname: Ye
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Chuanjun
authors.initials: C
authors.lastname: Liu
authors.affiliation: Howard Hughes Medical Institute, Department of Energy Plant Research Laboratory, and Department of Plant Biology, Michigan State University, East Lansing, MI, 48864, USA.
authors.forename: Xiufang
authors.initials: X
authors.lastname: Xin
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Chu-Yu
authors.initials: CY
authors.lastname: Ye
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Ying-Ying
authors.initials: YY
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Hongqing
authors.initials: H
authors.lastname: Xie
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Jiandong
authors.initials: J
authors.lastname: Bao
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: She
authors.initials: S
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xu
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Yijie
authors.initials: Y
authors.lastname: Gui
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Fu
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Weidi
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Xingchen
authors.initials: X
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Qianhua
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xuanmin
authors.initials: X
authors.lastname: Guang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Chongzhi
authors.initials: C
authors.lastname: Wang
authors.affiliation: College of Life Science, China Jiliang University, Hangzhou, 310018, China.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Cui
authors.affiliation: Department of Molecular Phytopathology, Christian-Albrechts-University of Kiel, D-24118, Kiel, Germany.
authors.forename: Daguang
authors.initials: D
authors.lastname: Cai
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
authors.forename: Song
authors.initials: S
authors.lastname: Ge
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Xiaohan
authors.initials: X
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
authors.affiliation: Howard Hughes Medical Institute, Department of Energy Plant Research Laboratory, and Department of Plant Biology, Michigan State University, East Lansing, MI, 48864, USA.
authors.forename: Sheng Yang
authors.initials: SY
authors.lastname: He
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Xue-Ping
authors.initials: XP
authors.lastname: Zhou
authors.affiliation: Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D060026:Endophytes / Q000472:pathogenicity*; D018745:Genome, Plant / Q000235:genetics*; D054884:Host-Pathogen Interactions / Q000235:genetics; D006109:Poaceae / Q000235:genetics* / Q000382:microbiology*
keywords: Jiaobai; Zizania; genome; host-microbe interaction; resistance gene analogs