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

dc.contributor.authorCheng, Shi-Ping
dc.contributor.authorJia, Kai-Hua
dc.contributor.authorLiu, Hui
dc.contributor.authorZhang, Ren-Gang
dc.contributor.authorLi, Zhi-Chao
dc.contributor.authorZhou, Shan-Shan
dc.contributor.authorShi, Tian-Le
dc.contributor.authorMa, Ai-Chu
dc.contributor.authorYu, Cong-Wen
dc.contributor.authorGao, Chan
dc.contributor.authorCao, Guang-Lei
dc.contributor.authorZhao, Wei
dc.contributor.authorNie, Shuai
dc.contributor.authorGuo, Jing-Fang
dc.contributor.authorJiao, Si-Qian
dc.contributor.authorTian, Xue-Chan
dc.contributor.authorYan, Xue-Mei
dc.contributor.authorBao, Yu-Tao
dc.contributor.authorYun, Quan-Zheng
dc.contributor.authorWang, Xin-Zhu
dc.contributor.authorPorth, Ilga
dc.contributor.authorEl-Kassaby, Yousry A.
dc.contributor.authorWang, Xiao-Ru
dc.contributor.authorLi, Zhen
dc.contributor.authorVan de Peer, Yves
dc.contributor.authorMao, Jian-Feng
dc.date.accessioned2022-05-20T10:54:07Z
dc.date.available2022-05-20T10:54:07Z
dc.date.issued2021-08
dc.description.abstractGinger (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.en_US
dc.description.departmentBiochemistryen_US
dc.description.departmentGeneticsen_US
dc.description.departmentMicrobiology and Plant Pathologyen_US
dc.description.librarianhj2022en_US
dc.description.urihttps://www.nature.com/hortresen_US
dc.identifier.citationCheng, SP., Jia, KH., Liu, H. et al. Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. Horticulture Research 8, 188 (2021). https://doi.org/10.1038/s41438-021-00599-8.en_US
dc.identifier.isbn10.1038/s41438-021-00599-8
dc.identifier.issn2662-6810 (print)
dc.identifier.issn2052-7276 (online)
dc.identifier.urihttps://repository.up.ac.za/handle/2263/85606
dc.language.isoenen_US
dc.publisherSpringer Natureen_US
dc.rights© 2021, The Author(s). Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License.en_US
dc.subjectGinger (Zingiber officinale)en_US
dc.subjectGene expressionen_US
dc.subjectGene regulationen_US
dc.subjectPlant evolutionen_US
dc.titleHaplotype-resolved genome assembly and allele-specific gene expression in cultivated gingeren_US
dc.typeArticleen_US

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