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.

Details

Title
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
Author
Shi-Ping, Cheng 1 ; Kai-Hua, Jia 2 ; Liu, Hui 2 ; Ren-Gang, Zhang 3 ; Zhi-Chao, Li 2 ; Shan-Shan, Zhou 2 ; Tian-Le, Shi 2 ; Ai-Chu, Ma 4 ; Cong-Wen, Yu 4 ; Chan, Gao 4 ; Guang-Lei, Cao 4 ; Zhao, Wei 5 ; Nie Shuai 2 ; Jing-Fang, Guo 2 ; Si-Qian, Jiao 2 ; Xue-Chan, Tian 2 ; Xue-Mei, Yan 2 ; Yu-Tao, Bao 2 ; Quan-Zheng, Yun 3 ; Xin-Zhu, Wang 3 ; Porth Ilga 6 ; El-Kassaby, Yousry A 7 ; Xiao-Ru, Wang 5 ; Li, Zhen 8 ; Van de Peer Yves 9 ; Jian-Feng, Mao 2   VIAFID ORCID Logo 

 Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, China (GRID:grid.449268.5) (ISNI:0000 0004 1797 3968) 
 Beijing Forestry University, Beijing 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, China (GRID:grid.66741.32) (ISNI:0000 0001 1456 856X) 
 Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, China (GRID:grid.66741.32) 
 Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China (GRID:grid.66741.32) 
 Beijing Forestry University, Beijing 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, China (GRID:grid.66741.32) (ISNI:0000 0001 1456 856X); UPSC, Umeå University, Department of Ecology and Environmental Science, Umeå, Sweden (GRID:grid.467081.c) (ISNI:0000 0004 0613 9724) 
 Université Laval Québec, Département des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Québec, Canada (GRID:grid.23856.3a) (ISNI:0000 0004 1936 8390) 
 University of British Columbia, Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, Canada (GRID:grid.17091.3e) (ISNI:0000 0001 2288 9830) 
 Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium (GRID:grid.5342.0) (ISNI:0000 0001 2069 7798); VIB Center for Plant Systems Biology, Ghent, Belgium (GRID:grid.511033.5) 
 Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium (GRID:grid.5342.0) (ISNI:0000 0001 2069 7798); VIB Center for Plant Systems Biology, Ghent, Belgium (GRID:grid.511033.5); University of Pretoria, Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, Pretoria, South Africa (GRID:grid.49697.35) (ISNI:0000 0001 2107 2298); Nanjing Agricultural University, College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing, China (GRID:grid.27871.3b) (ISNI:0000 0000 9750 7019) 
Publication year
2021
Publication date
2021
Publisher
Oxford University Press
e-ISSN
20527276
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2558265807
Copyright
© The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.