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Wang H, Yao G, Chen W, Ayhan DH, Wang X, Sun J, Yi S, Meng T, Chen S, Geng X, Meng D, Zhang L, Guo L. A gap-free genome assembly of Fusarium oxysporum f. sp. conglutinans, a vascular wilt pathogen. Sci Data 2024; 11:925. [PMID: 39191793 PMCID: PMC11349993 DOI: 10.1038/s41597-024-03763-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Fusarium oxysporum is an asexual filamentous fungus that causes vascular wilt in hundreds of crop plants and poses a threat to public health through Fusariosis. F. oxysporum f. sp. conglutinans strain Fo5176, originally isolated from Brassica oleracea, is pathogenic to Arabidopsis, making it a model pathosystem for dissecting the molecular mechanisms underlying host-pathogen interactions. Assembling the F. oxysporum genome is notoriously challenging due to the presence of repeat-rich accessory chromosomes. Here, we report a gap-free genome assembly of Fo5176 using PacBio HiFi and Hi-C data. The 69.56 Mb assembly contained 18 complete chromosomes, including all centromeres and most telomeres (20/36), representing the first gap-free genome sequence of a pathogenic F. oxysporum strain. In total, 21,460 protein-coding genes were annotated, a 26.3% increase compared to the most recent assembly. This high-quality reference genome for F. oxysporum f. sp. conglutinans Fo5176 provides a valuable resource for further research into fungal pathobiology and evolution.
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Affiliation(s)
- Huan Wang
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Gang Yao
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
- Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Weikai Chen
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Dilay Hazal Ayhan
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiangfeng Wang
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Jie Sun
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Shu Yi
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Tan Meng
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Shaoying Chen
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xin Geng
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Dian Meng
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Lili Zhang
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
- Weifang Institute of Technology, College of Modern Agriculture and Environment, Weifang, Shandong, 262500, China.
| | - Li Guo
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
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Amas JC, Thomas WJW, Zhang Y, Edwards D, Batley J. Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species. PHYTOPATHOLOGY 2023:PHYTO08220289FI. [PMID: 36324059 DOI: 10.1094/phyto-08-22-0289-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.
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Affiliation(s)
- Junrey C Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - William J W Thomas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Yueqi Zhang
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
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Asai S, Ayukawa Y, Gan P, Shirasu K. Draft Genome Resources for Brassicaceae Pathogens Fusarium oxysporum f. sp. raphani and Fusarium oxysporum f. sp. rapae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1316-1319. [PMID: 34289713 DOI: 10.1094/mpmi-06-21-0148-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The soilborne filamentous fungus Fusarium oxysporum causes devastating diseases of many cultivated plant species. F. oxysporum f. sp. raphani and f. sp. rapae are two of four formae speciales that are pathogenic to Brassicaceae plants. Here, we present high-quality genome sequences of F. oxysporum f. sp. raphani strain Tf1262 and F. oxysporum f. sp. rapae strain Tf1208 that were isolated from radish (Raphanus sativus) and turnip (Brassica rapa var. rapa), respectively. These genome resources should facilitate in-depth investigation of interactions between F. oxysporum and Brassicaceae plants, and enable comparative genomics of the F. oxysporum species complex to uncover how pathogenicity evolved within F. oxysporum.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Shuta Asai
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Yu Ayukawa
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
| | - Pamela Gan
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan
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Liu Z, Wang H, Xie J, Lv J, Zhang G, Hu L, Luo S, Li L, Yu J. The Roles of Cruciferae Glucosinolates in Disease and Pest Resistance. PLANTS 2021; 10:plants10061097. [PMID: 34070720 PMCID: PMC8229868 DOI: 10.3390/plants10061097] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/17/2022]
Abstract
With the expansion of the area under Cruciferae vegetable cultivation, and an increase in the incidence of natural threats such as pests and diseases globally, Cruciferae vegetable losses caused by pathogens, insects, and pests are on the rise. As one of the key metabolites produced by Cruciferae vegetables, glucosinolate (GLS) is not only an indicator of their quality but also controls infestation by numerous fungi, bacteria, aphids, and worms. Today, the safe and pollution-free production of vegetables is advocated globally, and environmentally friendly pest and disease control strategies, such as biological control, to minimize the adverse impacts of pathogen and insect pest stress on Cruciferae vegetables, have attracted the attention of researchers. This review explores the mechanisms via which GLS acts as a defensive substance, participates in responses to biotic stress, and enhances plant tolerance to the various stress factors. According to the current research status, future research directions are also proposed.
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Affiliation(s)
- Zeci Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China;
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Huiping Wang
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Jianming Xie
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Jian Lv
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Guobin Zhang
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Linli Hu
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Shilei Luo
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
| | - Lushan Li
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua 617000, China
| | - Jihua Yu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China;
- College of Horticulture, Gansu Agriculture University, Lanzhou 730070, China; (H.W.); (J.X.); (J.L.); (G.Z.); (L.H.); (S.L.); (L.L.)
- Correspondence: ; Tel.: +86-931-763-2188
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