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Fu A, Wang Q, Mu J, Ma L, Wen C, Zhao X, Gao L, Li J, Shi K, Wang Y, Zhang X, Zhang X, Wang F, Grierson D, Zuo J. Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development. HORTICULTURE RESEARCH 2021; 8:35. [PMID: 33517348 PMCID: PMC7847470 DOI: 10.1038/s41438-021-00487-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 05/11/2023]
Abstract
Chayote (Sechium edule) is an agricultural crop in the Cucurbitaceae family that is rich in bioactive components. To enhance genetic research on chayote, we used Nanopore third-generation sequencing combined with Hi-C data to assemble a draft chayote genome. A chromosome-level assembly anchored on 14 chromosomes (N50 contig and scaffold sizes of 8.40 and 46.56 Mb, respectively) estimated the genome size as 606.42 Mb, which is large for the Cucurbitaceae, with 65.94% (401.08 Mb) of the genome comprising repetitive sequences; 28,237 protein-coding genes were predicted. Comparative genome analysis indicated that chayote and snake gourd diverged from sponge gourd and that a whole-genome duplication (WGD) event occurred in chayote at 25 ± 4 Mya. Transcriptional and metabolic analysis revealed genes involved in fruit texture, pigment, flavor, flavonoids, antioxidants, and plant hormones during chayote fruit development. The analysis of the genome, transcriptome, and metabolome provides insights into chayote evolution and lays the groundwork for future research on fruit and tuber development and genetic improvements in chayote.
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Affiliation(s)
- Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jianlou Mu
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Xuechuan Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Xuewen Zhang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Fengling Wang
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, The Collaborative Innovation Center of Cucurbits Crops, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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