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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
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 p...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342452/ https://www.ncbi.nlm.nih.gov/pubmed/34354050 http://dx.doi.org/10.1038/s41438-021-00599-8 |
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author | Cheng, Shi-Ping Jia, Kai-Hua Liu, Hui Zhang, Ren-Gang Li, Zhi-Chao Zhou, Shan-Shan Shi, Tian-Le Ma, Ai-Chu Yu, Cong-Wen Gao, Chan Cao, Guang-Lei Zhao, Wei Nie, Shuai Guo, Jing-Fang Jiao, Si-Qian Tian, Xue-Chan Yan, Xue-Mei Bao, Yu-Tao Yun, Quan-Zheng Wang, Xin-Zhu Porth, Ilga El-Kassaby, Yousry A. Wang, Xiao-Ru Li, Zhen Van de Peer, Yves Mao, Jian-Feng |
author_facet | Cheng, Shi-Ping Jia, Kai-Hua Liu, Hui Zhang, Ren-Gang Li, Zhi-Chao Zhou, Shan-Shan Shi, Tian-Le Ma, Ai-Chu Yu, Cong-Wen Gao, Chan Cao, Guang-Lei Zhao, Wei Nie, Shuai Guo, Jing-Fang Jiao, Si-Qian Tian, Xue-Chan Yan, Xue-Mei Bao, Yu-Tao Yun, Quan-Zheng Wang, Xin-Zhu Porth, Ilga El-Kassaby, Yousry A. Wang, Xiao-Ru Li, Zhen Van de Peer, Yves Mao, Jian-Feng |
author_sort | Cheng, Shi-Ping |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8342452 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-83424522021-08-20 Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger Cheng, Shi-Ping Jia, Kai-Hua Liu, Hui Zhang, Ren-Gang Li, Zhi-Chao Zhou, Shan-Shan Shi, Tian-Le Ma, Ai-Chu Yu, Cong-Wen Gao, Chan Cao, Guang-Lei Zhao, Wei Nie, Shuai Guo, Jing-Fang Jiao, Si-Qian Tian, Xue-Chan Yan, Xue-Mei Bao, Yu-Tao Yun, Quan-Zheng Wang, Xin-Zhu Porth, Ilga El-Kassaby, Yousry A. Wang, Xiao-Ru Li, Zhen Van de Peer, Yves Mao, Jian-Feng Hortic Res Article 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. Nature Publishing Group UK 2021-08-05 /pmc/articles/PMC8342452/ /pubmed/34354050 http://dx.doi.org/10.1038/s41438-021-00599-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Cheng, Shi-Ping Jia, Kai-Hua Liu, Hui Zhang, Ren-Gang Li, Zhi-Chao Zhou, Shan-Shan Shi, Tian-Le Ma, Ai-Chu Yu, Cong-Wen Gao, Chan Cao, Guang-Lei Zhao, Wei Nie, Shuai Guo, Jing-Fang Jiao, Si-Qian Tian, Xue-Chan Yan, Xue-Mei Bao, Yu-Tao Yun, Quan-Zheng Wang, Xin-Zhu Porth, Ilga El-Kassaby, Yousry A. Wang, Xiao-Ru Li, Zhen Van de Peer, Yves Mao, Jian-Feng Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger |
title | Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger |
title_full | Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger |
title_fullStr | Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger |
title_full_unstemmed | Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger |
title_short | Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger |
title_sort | haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342452/ https://www.ncbi.nlm.nih.gov/pubmed/34354050 http://dx.doi.org/10.1038/s41438-021-00599-8 |
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