Haplotype-resolved genome assembly and allele- specific gene expression in cultivated ginger
作者机构：Pingdingshan UniversityHenan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody PlantPingdingshan 467000 HenanChina Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Ori(Shandong)Gene Science and Technology Co.LtdWeifang 261000 ShandongChina Pingdingshan Academy of Agricultural SciencesPingdingshan 467000 HenanChina Department of Ecology and Environmental ScienceUPSCUmea UniversityUmeaSweden Departement des Sciences du Bois et de la ForetFacultede Foresteriede Geographie et GéomatiqueUniversite Laval QuebecQuebecQC G1V 0A6Canada Department of Forest and Conservation SciencesFaculty of ForestryUniversity of British ColumbiaVancouverBC V6T 1Z4Canada Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium VIB Center for Plant Systems Biology9052 GhentBelgium Centre for Microbial Ecology and GenomicsDepartment of BiochemistryGenetics and Microbiology GeneticsUniversity of PretoriaPrivate Bag X20Pretoria 0028South Africa College of HorticultureAcademy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China
出 版 物：《Horticulture Research》 (园艺研究（英文）)
年 卷 期：2021年第8卷第1期
页 面：2531-2545页
核心收录：
学科分类：0710[理学-生物学] 0831[工学-生物医学工程（可授工学、理学、医学学位）] 1001[医学-基础医学(可授医学、理学学位)] 09[农学] 0901[农学-作物学] 0703[理学-化学] 0836[工学-生物工程] 0902[农学-园艺学] 0834[工学-风景园林学（可授工学、农学学位）] 090202[农学-蔬菜学]
基 金：This study was supported by the Foundation for the Introduction of Talent of Pingdingshan University(PXY-BSQD2016009) the Key Research Project of Colleges and Universities of Henan Province(182102110132,172102110111) the National Natural Science Foundation(31600527) the Fundamental Research Funds for the Central Universities of Beijing Forestry University(2018BLCB08) the Project for the Construction of World Class Universities of Beijing Forestry University(2019XKJS0308) the Scientific Research Foundation for National Natural Science Fund(31600527) Z.L.is funded by a postdoctoral fellowship from the Special Research Fund of Ghent University(BOFPDO2018001701) Y.V.P.acknowledges fundings from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(grant agreement No 833522) from Ghent University(Methusalem funding,BOF.MET.2021.0005.01)
摘 要：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 ***,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 *** structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger *** performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately *** 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 *** also predicted the transcription factors potentially regulating 6-gingerol *** allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.
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