Heliyon (Feb 2021)
Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops
- Rui-Fang Gao,
- Jie-Yu Wang,
- Ke-Wei Liu,
- Kouki Yoshida,
- Yu-Yun Hsiao,
- Yi-Xiang Shi,
- Kun-Chan Tsai,
- You-Yi Chen,
- Nobutaka Mitsuda,
- Chieh-Kai Liang,
- Zhi-Wen Wang,
- Ying Wang,
- Di-Yang Zhang,
- Laiqiang Huang,
- Xiang Zhao,
- Wen-Ying Zhong,
- Ying-Hui Cheng,
- Zi-De Jiang,
- Ming-He Li,
- Wei-Hong Sun,
- Xia Yu,
- Wenqi Hu,
- Zhuang Zhou,
- Xiao-Fan Zhou,
- Chuan-Ming Yeh,
- Kazutaka Katoh,
- Wen-Chieh Tsai,
- Zhong-Jian Liu,
- Francis Martin,
- Gui-Ming Zhang
Affiliations
- Rui-Fang Gao
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen 518045, China; Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen 518045, China
- Jie-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Ke-Wei Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy State Key Laboratory of Health Sciences and Technology (prep), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Center for Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute (TBSI), Shenzhen 518055, China
- Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa 245-0051, Japan
- Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
- Yi-Xiang Shi
- Shanghai Major Bio-pharm Technology Co., Ltd., Shanghai 201203, China
- Kun-Chan Tsai
- Reber Genetics Co., Ltd., Taipei 10685, Taiwan
- You-Yi Chen
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
- Chieh-Kai Liang
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
- Ying Wang
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen 518045, China; Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen 518045, China
- Di-Yang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Laiqiang Huang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy State Key Laboratory of Health Sciences and Technology (prep), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan 430070, China
- Wen-Ying Zhong
- PubBio-Tech Services Corporation, Wuhan 430070, China
- Ying-Hui Cheng
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China
- Zi-De Jiang
- College of Agriculture, South China Agricultural University, Guangzhou 510640, China
- Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Wei-Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Wenqi Hu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Zhuang Zhou
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China
- Xiao-Fan Zhou
- College of Agriculture, South China Agricultural University, Guangzhou 510640, China
- Chuan-Ming Yeh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan; Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan; Corresponding author.
- Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Corresponding author.
- Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan; Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan; Corresponding author.
- Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy State Key Laboratory of Health Sciences and Technology (prep), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou 325005, China; Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, 250100, Jinan, China; Corresponding author.
- Francis Martin
- Institut National de la Recherche Agronomique, UMR Interactions Arbres/Microorganismes, Centre INRA Grand Est-Nancy, Université de Lorraine, 54280 Champenoux, France; Corresponding author.
- Gui-Ming Zhang
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen 518045, China; Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen 518045, China; Corresponding author.
- Journal volume & issue
-
Vol. 7,
no. 2
p. e06317
Abstract
The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species–P. fragariae and P. rubi. Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that “transmit” exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies.
