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 *Corresponding author. E-mail: nevernever107@126.com,jianjianbo@genomics.cn,xiaqy@swu.edu.cn,liung906@163.com
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.