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Article|31 Jan 2021|OPEN
Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development
Anzhen Fu1,2, Qing Wang1, Jianlou Mu2, Lili Ma1,2, Changlong Wen1, Xiaoyan Zhao1, Lipu Gao1, Jian Li3, Kai Shi4, Yunxiang Wang5, Xuechuan Zhang6, Xuewen Zhang6, Fengling Wang6, Donald Grierson7 & Jinhua Zuo1,
1Key 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
2College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China
3Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
4Department of Horticulture, Zhejiang University, Hangzhou 310058, China
5Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
6Biomarker Technologies Corporation, Beijing 101300, China
7School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK

Horticulture Research 8,
Article number: 35 (2021)
doi: 10.1038/hortres.2021.35
Views: 1056

Received: 23 Jul 2020
Revised: 07 Jan 2021
Accepted: 07 Jan 2021
Published online: 31 Jan 2021

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.