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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger

Cheng, Shi-Ping (författare)
Pingdingshan University, Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Henan, Pingdingshan, China
Jia, Kai-Hua (författare)
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 Forestry University, Beijing, China
Liu, Hui (författare)
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 Forestry University, Beijing, China
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Zhang, Ren-Gang (författare)
Ori (Shandong) Gene Science and Technology Co., Ltd, Shandong, Weifang, China
Li, Zhi-Chao (författare)
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 Forestry University, Beijing, China
Zhou, Shan-Shan (författare)
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 Forestry University, Beijing, China
Shi, Tian-Le (författare)
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 Forestry University, Beijing, China
Ma, Ai-Chu (författare)
Pingdingshan Academy of Agricultural Sciences, Henan, Pingdingshan, China
Yu, Cong-Wen (författare)
Pingdingshan Academy of Agricultural Sciences, Henan, Pingdingshan, China
Gao, Chan (författare)
Pingdingshan Academy of Agricultural Sciences, Henan, Pingdingshan, China
Cao, Guang-Lei (författare)
Pingdingshan Academy of Agricultural Sciences, Henan, Pingdingshan, China
Zhao, Wei (författare)
Umeå universitet,Institutionen för ekologi, miljö och geovetenskap,Umeå Plant Science Centre (UPSC),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 Forestry University, Beijing, China
Nie, Shuai (författare)
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 Forestry University, Beijing, China
Guo, Jing-Fang (författare)
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 Forestry University, Beijing, China
Jiao, Si-Qian (författare)
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 Forestry University, Beijing, China
Tian, Xue-Chan (författare)
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 Forestry University, Beijing, China
Yan, Xue-Mei (författare)
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 Forestry University, Beijing, China
Bao, Yu-Tao (författare)
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 Forestry University, Beijing, China
Yun, Quan-Zheng (författare)
Ori (Shandong) Gene Science and Technology Co., Ltd, Shandong, Weifang, China
Wang, Xin-Zhu (författare)
Ori (Shandong) Gene Science and Technology Co., Ltd, Shandong, Weifang, China
Porth, Ilga (författare)
Département des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval Québec, QC, Québec, Canada
El-Kassaby, Yousry A. (författare)
Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, BC, Vancouver, Canada
Wang, Xiao-Ru (författare)
Umeå universitet,Institutionen för ekologi, miljö och geovetenskap,Umeå Plant Science Centre (UPSC),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 Forestry University, Beijing, China
Li, Zhen (författare)
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
Van de Peer, Yves (författare)
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private Bag X20, Pretoria, South Africa; College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
Mao, Jian-Feng (författare)
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 Forestry University, Beijing, China
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 (creator_code:org_t)
Springer Nature, 2021
2021
Engelska.
Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
Stäng  
  • 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.

Ämnesord

NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)
NATURVETENSKAP  -- Biologiska vetenskaper -- Genetik (hsv//swe)
NATURVETENSKAP  -- Biologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences (hsv//eng)

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