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Article|05 Aug 2021|OPEN
Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway
Hong-Lei Li1,2, Lin Wu1,2, Zhaoming Dong3, Yusong Jiang1,2, Sanjie Jiang4, Haitao Xing1,2, Qiang Li1,2, Guocheng Liu4, Shuming Tian1,5, Zhangyan Wu4, Bin Wu4, Zhexin Li1,2, Ping Zhao3, Yan Zhang3, Jianmin Tang1,2, Jiabao Xu4, Ke Huang1,2, Xia Liu1,2, Wenlin Zhang1,2, Qinhong Liao1,2, Yun Ren1,2, Xinzheng Huang6, Qingzhi Li7, Chengyong Li7, Yi Wang3, Baskaran Xavier-Ravi8, Honghai Li9, Yang Liu4,10, Tao Wan10, Qinhu Liu11, Yong Zou 2,1,, Yiqing Liu12,1,, Jianbo Jian4, & Qingyou Xia3,
1College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
2Engineering Research Center for Special Plant Seedlings of Chongqing, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
3State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing, China
4BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
5College of Biology and Food Engineering, Chongqign Three Gorges University, Wanzhou, Chongqing, China
6Department of Entomology and MOAKey Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian, Beijing, China
7Jinan Second Agricultural Science Research Institute, Jinan, Shandong, China
8Savari Research Foundation, Mela Ilandai Kulam, Tamil Nadu, India
9Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
10Fairy Lake Botanical Garden and Chinese Academy of Sciences, Shenzhen, Guangdong, China
11Ningyang Science and Technology Bureau, Taian, Shandong, China
12College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China

Horticulture Research 8,
Article number: 189 (2021)
doi: 10.1038/hortres.2021.189
Views: 23

Received: 13 Apr 2021
Revised: 20 Jun 2021
Accepted: 13 Jul 2021
Published online: 05 Aug 2021

Abstract

Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.