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

doi:10.1186/s12864-019-5734-x

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

Journal Article · 27 May 2019 · BMC Genomics

DOI: https://doi.org/10.1186/s12864-019-5734-x · OSTI ID:1618572

^[1]; Brenton, Zachary W. ^[2]; Flinn, Barry S. ^[2]; Jenkins, Jerry ^[3]; Shu, Shengqiang ^[4]; Flowers, Dave ^[3]; Luo, Feng ^[2]; Wang, Yunsheng ^[5]; Xia, Penny ^[2]; Barry, Kerrie ^[4]; Daum, Chris ^[4]; Lipzen, Anna ^[4]; Yoshinaga, Yuko ^[4]; Schmutz, Jeremy ^[6]; Saski, Christopher ^[2]; Vermerris, Wilfred ^[7]; Kresovich, Stephen ^[2]

Clemson Univ., Clemson, SC (United States); Univ. of North Carolina at Charlotte, Charlotte, NC (United States)
Clemson Univ., Clemson, SC (United States)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Clemson Univ., Clemson, SC (United States); Hunan Agricultural Univ., Changsha (China)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of Florida, Gainesville, FL (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); USDOE

Grant/Contract Number:: AC02-05CH11231; FG02-07ER64458; AR0000595

OSTI ID:: 1618572

Alternate ID(s):: OSTI ID: 1572011

Journal Information:: BMC Genomics, Vol. 20, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 10: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190719 The current record is supplemented by this dataset	dataset	January 2019
Additional file 10: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190719.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 1: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190728 The current record is supplemented by this text	text	January 2019
Additional file 1: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190728.v1 The current record is supplemented by this text	text	January 2019
Additional file 2: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190734 The current record is supplemented by this text	text	January 2019
Additional file 2: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190734.v1 The current record is supplemented by this text	text	January 2019
Additional file 3: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190740 The current record is supplemented by this dataset	dataset	January 2019
Additional file 3: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190740.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 4: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190743 The current record is supplemented by this dataset	dataset	January 2019
Additional file 4: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190743.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 5: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190749 The current record is supplemented by this dataset	dataset	January 2019
Additional file 5: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190749.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 6: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190755 The current record is supplemented by this dataset	dataset	January 2019
Additional file 6: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190755.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 7: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190758 The current record is supplemented by this dataset	dataset	January 2019
Additional file 7: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190758.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 8: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190764 The current record is supplemented by this dataset	dataset	January 2019
Additional file 8: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190764.v1 The current record is supplemented by this dataset	dataset	January 2019
Additional file 9: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190776 The current record is supplemented by this dataset	dataset	January 2019
Additional file 9: of 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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.8190776.v1 The current record is supplemented by this dataset	dataset	January 2019
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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.c.4519544 The current record is supplemented by this collection	collection	January 2019
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; Brenton, Zachary; Flinn, Barry https://doi.org/10.6084/m9.figshare.c.4519544.v1 The current record is supplemented by this collection	collection	January 2019

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

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