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03 06, 2020;21 (1): 60.

The genome evolution and domestication of tropical fruit mango.

Peng Wang, Yingfeng Luo, Jianfeng Huang, Shenghan Gao, Guopeng Zhu, Zhiguo Dang, Jiangtao Gai, Meng Yang, Min Zhu, Huangkai Zhang, Xiuxu Ye, Aiping Gao, Xinyu Tan, Sen Wang, Shuangyang Wu, Edgar B Cahoon, Beibei Bai, Zhichang Zhao, Qian Li, Junya Wei, Huarui Chen, Ruixiong Luo, Deyong Gong, Kexuan Tang, Bing Zhang, Zhangguang Ni, Guodi Huang, Songnian Hu, Yeyuan Chen
Author Information
  1. Peng Wang: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China. pwang@catas.cn. ORCID
  2. Yingfeng Luo: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.
  3. Jianfeng Huang: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  4. Shenghan Gao: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.
  5. Guopeng Zhu: School of Landscape and Horticulture, Hainan University, Haikou, 570208, Hainan, China.
  6. Zhiguo Dang: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  7. Jiangtao Gai: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  8. Meng Yang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  9. Min Zhu: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  10. Huangkai Zhang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  11. Xiuxu Ye: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  12. Aiping Gao: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  13. Xinyu Tan: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China.
  14. Sen Wang: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  15. Shuangyang Wu: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  16. Edgar B Cahoon: Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
  17. Beibei Bai: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  18. Zhichang Zhao: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  19. Qian Li: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  20. Junya Wei: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  21. Huarui Chen: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  22. Ruixiong Luo: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China.
  23. Deyong Gong: Guizhou Subtropical Crops Research Institute, Xingyi, Qianxinan, Guzhou, 562400, China.
  24. Kexuan Tang: Joint International Research Laboratory of Metabolic & Developmental Sciences, Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
  25. Bing Zhang: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
  26. Zhangguang Ni: Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, 678005, Yunnan, China.
  27. Guodi Huang: Guangxi Subtropical Crops Research Institute, Nanning, 530001, Guangxi, China.
  28. Songnian Hu: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1-3 West Beichen Road, Beijing, 100101, China. husn@im.ac.cn.
  29. Yeyuan Chen: Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou, 571100, Hainan, China. chenyy1962@catas.cn.
PMID: 32143734 DOI: 10.1186/s13059-020-01959-8

Abstract

BACKGROUND: Mango is one of the world's most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis.
RESULTS: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes.
CONCLUSIONS: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces.

Keywords

Germplasm Mango genome Photosynthesis Urushiol Whole-genome duplication

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MeSH Term

Acyltransferases
Domestication
Evolution, Molecular
Fruit
Genetic Variation
Genome, Plant
Mangifera
Phenols
Pigmentation

Chemicals

Phenols
Acyltransferases
flavanone synthetase
Journal Article Research Support, Non-U.S. Gov't

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