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Article|05 Aug 2021|OPEN
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
Shi-Ping Cheng1, Kai-Hua Jia2, Hui Liu2, Zhi-Chao Li2, Shan-Shan Zhou2, Ren-Gang Zhang3, Tian-Le Shi2, Ai-Chu Ma4, Cong-Wen Yu4, Chan Gao4, Guang-Lei Cao4, Wei Zhao2,5, Shuai Nie2, Jing-Fang Guo2, Si-Qian Jiao2, Xue-Chan Tian2, Xue-Mei Yan2, Yu-Tao Bao2, Quan-Zheng Yun3, Xin-Zhu Wang3, Ilga Porth6, Xiao-Ru Wang2,5, Yousry A. El-Kassaby7, Zhen Li8,9, Yves Van de Peer9,10,11,8, & Jian-Feng Mao 2,
1Pingdingshan University, Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan 467000 Henan, China
2Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
3Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang 261000 Shandong, China
4Pingdingshan Academy of Agricultural Sciences, Pingdingshan 467000 Henan, China
5Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden
6Département des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval Québec, Québec, QC G1V 0A6, Canada
7Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
8Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
9VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
10Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
11College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China

Horticulture Research 8,
Article number: 188 (2021)
doi: 10.1038/hortres.2021.188
Views: 27

Received: 08 Jan 2021
Revised: 18 Apr 2021
Accepted: 11 May 2021
Published online: 05 Aug 2021

Abstract

Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.