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A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism
BACKGROUND: The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure t...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537160/ https://www.ncbi.nlm.nih.gov/pubmed/31133004 http://dx.doi.org/10.1186/s12864-019-5734-x |
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author | Cooper, Elizabeth A. Brenton, Zachary W. Flinn, Barry S. Jenkins, Jerry Shu, Shengqiang Flowers, Dave Luo, Feng Wang, Yunsheng Xia, Penny Barry, Kerrie Daum, Chris Lipzen, Anna Yoshinaga, Yuko Schmutz, Jeremy Saski, Christopher Vermerris, Wilfred Kresovich, Stephen |
author_facet | Cooper, Elizabeth A. Brenton, Zachary W. Flinn, Barry S. Jenkins, Jerry Shu, Shengqiang Flowers, Dave Luo, Feng Wang, Yunsheng Xia, Penny Barry, Kerrie Daum, Chris Lipzen, Anna Yoshinaga, Yuko Schmutz, Jeremy Saski, Christopher Vermerris, Wilfred Kresovich, Stephen |
author_sort | Cooper, Elizabeth A. |
collection | PubMed |
description | BACKGROUND: The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure to increase sugar accumulation in certain varieties of the cereal crop Sorghum bicolor is an excellent example of the latter; this has resulted in pronounced phenotypic divergence between sweet and grain-type sorghums, but the genetic mechanisms underlying these differences remain poorly understood. RESULTS: Here we present a new reference genome based on an archetypal sweet sorghum line and compare it to the current grain sorghum reference, revealing a high rate of nonsynonymous and potential loss of function mutations, but few changes in gene content or overall genome structure. We also use comparative transcriptomics to highlight changes in gene expression correlated with high stalk sugar content and show that changes in the activity and possibly localization of transporters, along with the timing of sugar metabolism play a critical role in the sweet phenotype. CONCLUSIONS: The high level of genomic similarity between sweet and grain sorghum reflects their historical relatedness, rather than their current phenotypic differences, but we find key changes in signaling molecules and transcriptional regulators that represent new candidates for understanding and improving sugar metabolism in this important crop. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5734-x) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6537160 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65371602019-05-30 A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism Cooper, Elizabeth A. Brenton, Zachary W. Flinn, Barry S. Jenkins, Jerry Shu, Shengqiang Flowers, Dave Luo, Feng Wang, Yunsheng Xia, Penny Barry, Kerrie Daum, Chris Lipzen, Anna Yoshinaga, Yuko Schmutz, Jeremy Saski, Christopher Vermerris, Wilfred Kresovich, Stephen BMC Genomics Research Article BACKGROUND: The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure to increase sugar accumulation in certain varieties of the cereal crop Sorghum bicolor is an excellent example of the latter; this has resulted in pronounced phenotypic divergence between sweet and grain-type sorghums, but the genetic mechanisms underlying these differences remain poorly understood. RESULTS: Here we present a new reference genome based on an archetypal sweet sorghum line and compare it to the current grain sorghum reference, revealing a high rate of nonsynonymous and potential loss of function mutations, but few changes in gene content or overall genome structure. We also use comparative transcriptomics to highlight changes in gene expression correlated with high stalk sugar content and show that changes in the activity and possibly localization of transporters, along with the timing of sugar metabolism play a critical role in the sweet phenotype. CONCLUSIONS: The high level of genomic similarity between sweet and grain sorghum reflects their historical relatedness, rather than their current phenotypic differences, but we find key changes in signaling molecules and transcriptional regulators that represent new candidates for understanding and improving sugar metabolism in this important crop. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5734-x) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-27 /pmc/articles/PMC6537160/ /pubmed/31133004 http://dx.doi.org/10.1186/s12864-019-5734-x Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Cooper, Elizabeth A. Brenton, Zachary W. Flinn, Barry S. Jenkins, Jerry Shu, Shengqiang Flowers, Dave Luo, Feng Wang, Yunsheng Xia, Penny Barry, Kerrie Daum, Chris Lipzen, Anna Yoshinaga, Yuko Schmutz, Jeremy Saski, Christopher Vermerris, Wilfred Kresovich, Stephen A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism |
title | A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism |
title_full | A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism |
title_fullStr | A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism |
title_full_unstemmed | A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism |
title_short | A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism |
title_sort | new reference genome for sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537160/ https://www.ncbi.nlm.nih.gov/pubmed/31133004 http://dx.doi.org/10.1186/s12864-019-5734-x |
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