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The Sorghum bicolor reference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization

Ryan F. McCormick, Sandra K. Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock Weers, Brian McKinley, Ashley Mattison, Daryl Morishige, Jane Grimwood, Jeremy Schmutz, John Mullet
doi: https://doi.org/10.1101/110593
Ryan F. McCormick
1Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX 77843, USA
2Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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Sandra K. Truong
1Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX 77843, USA
2Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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Avinash Sreedasyam
3HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Jerry Jenkins
3HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Shengqiang Shu
4Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598, USA
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David Sims
3HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Megan Kennedy
4Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598, USA
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Mojgan Amirebrahimi
4Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598, USA
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Brock Weers
2Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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Brian McKinley
2Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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Ashley Mattison
1Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX 77843, USA
2Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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Daryl Morishige
2Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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Jane Grimwood
3HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
4Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598, USA
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Jeremy Schmutz
3HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
4Joint Genome Institute, Department of Energy, Walnut Creek, CA 94598, USA
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John Mullet
2Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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2 ABSTRACT

Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Sub-telomeric repeats with characteristics of Tandem Repeats In Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of the reference genome sequence to 56 resequenced genomes from diverse sorghum genotypes identified ~7.4M SNPs and 1.8M indels. Large scale variant features in euchromatin were identified with periodicities of ~25 kbp. An RNA transcriptome atlas of gene expression was constructed from 47 samples derived from growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 21, 2017.
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The Sorghum bicolor reference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization
Ryan F. McCormick, Sandra K. Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock Weers, Brian McKinley, Ashley Mattison, Daryl Morishige, Jane Grimwood, Jeremy Schmutz, John Mullet
bioRxiv 110593; doi: https://doi.org/10.1101/110593
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The Sorghum bicolor reference genome: improved assembly and annotations, a transcriptome atlas, and signatures of genome organization
Ryan F. McCormick, Sandra K. Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock Weers, Brian McKinley, Ashley Mattison, Daryl Morishige, Jane Grimwood, Jeremy Schmutz, John Mullet
bioRxiv 110593; doi: https://doi.org/10.1101/110593

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