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Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway
Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342499/ https://www.ncbi.nlm.nih.gov/pubmed/34354044 http://dx.doi.org/10.1038/s41438-021-00627-7 |
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author | Li, Hong-Lei Wu, Lin Dong, Zhaoming Jiang, Yusong Jiang, Sanjie Xing, Haitao Li, Qiang Liu, Guocheng Tian, Shuming Wu, Zhangyan Bin Wu Li, Zhexin Zhao, Ping Zhang, Yan Tang, Jianmin Xu, Jiabao Huang, Ke Liu, Xia Zhang, Wenlin Liao, Qinhong Ren, Yun Huang, Xinzheng Li, Qingzhi Li, Chengyong Wang, Yi Xavier-Ravi, Baskaran Li, Honghai Liu, Yang Wan, Tao Liu, Qinhu Zou, Yong Jian, Jianbo Xia, Qingyou Liu, Yiqing |
author_facet | Li, Hong-Lei Wu, Lin Dong, Zhaoming Jiang, Yusong Jiang, Sanjie Xing, Haitao Li, Qiang Liu, Guocheng Tian, Shuming Wu, Zhangyan Bin Wu Li, Zhexin Zhao, Ping Zhang, Yan Tang, Jianmin Xu, Jiabao Huang, Ke Liu, Xia Zhang, Wenlin Liao, Qinhong Ren, Yun Huang, Xinzheng Li, Qingzhi Li, Chengyong Wang, Yi Xavier-Ravi, Baskaran Li, Honghai Liu, Yang Wan, Tao Liu, Qinhu Zou, Yong Jian, Jianbo Xia, Qingyou Liu, Yiqing |
author_sort | Li, Hong-Lei |
collection | PubMed |
description | Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis. |
format | Online Article Text |
id | pubmed-8342499 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-83424992021-08-20 Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway Li, Hong-Lei Wu, Lin Dong, Zhaoming Jiang, Yusong Jiang, Sanjie Xing, Haitao Li, Qiang Liu, Guocheng Tian, Shuming Wu, Zhangyan Bin Wu Li, Zhexin Zhao, Ping Zhang, Yan Tang, Jianmin Xu, Jiabao Huang, Ke Liu, Xia Zhang, Wenlin Liao, Qinhong Ren, Yun Huang, Xinzheng Li, Qingzhi Li, Chengyong Wang, Yi Xavier-Ravi, Baskaran Li, Honghai Liu, Yang Wan, Tao Liu, Qinhu Zou, Yong Jian, Jianbo Xia, Qingyou Liu, Yiqing Hortic Res Article Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis. Nature Publishing Group UK 2021-08-05 /pmc/articles/PMC8342499/ /pubmed/34354044 http://dx.doi.org/10.1038/s41438-021-00627-7 Text en © The Author(s) 2021, corrected publication 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 Li, Hong-Lei Wu, Lin Dong, Zhaoming Jiang, Yusong Jiang, Sanjie Xing, Haitao Li, Qiang Liu, Guocheng Tian, Shuming Wu, Zhangyan Bin Wu Li, Zhexin Zhao, Ping Zhang, Yan Tang, Jianmin Xu, Jiabao Huang, Ke Liu, Xia Zhang, Wenlin Liao, Qinhong Ren, Yun Huang, Xinzheng Li, Qingzhi Li, Chengyong Wang, Yi Xavier-Ravi, Baskaran Li, Honghai Liu, Yang Wan, Tao Liu, Qinhu Zou, Yong Jian, Jianbo Xia, Qingyou Liu, Yiqing Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway |
title | Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway |
title_full | Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway |
title_fullStr | Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway |
title_full_unstemmed | Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway |
title_short | Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway |
title_sort | haplotype-resolved genome of diploid ginger (zingiber officinale) and its unique gingerol biosynthetic pathway |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8342499/ https://www.ncbi.nlm.nih.gov/pubmed/34354044 http://dx.doi.org/10.1038/s41438-021-00627-7 |
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