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

Abstract

Summary Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 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. Subtelomeric 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 more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms ( SNP s) and 1.9 M indels. Large‐scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA ‐seq profiles of growing and developedmore » tissues of the major plant organs (roots, leaves, stems, panicles, and 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.« less

Authors:
 [1];  [1];  [2];  [2];  [3];  [2];  [3];  [3];  [1];  [1];  [1];  [1];  [4];  [4];  [1]
+ Show Author Affiliations
  1. Texas A & M Univ., College Station, TX (United States)
  2. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1616057
Alternate Identifier(s):
OSTI ID: 1415049
Grant/Contract Number:  
AC02-05CH11231; FC02-07ER64494; AR0000596; SC0012629; DE‐FC02‐07ER64494; DE‐AC02‐05CH11231; DE‐AR0000596; DE‐SC0012629
Resource Type:
Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Volume: 93; Journal Issue: 2; Journal ID: ISSN 0960-7412
Publisher:
Society for Experimental Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Sorghum bicolor; discrete Fourier transform; gene annotation; genetic variation; genome assembly; kinase; nucleosome occupancy; reference genome; satellite DNA

Citation Formats

McCormick, Ryan F., Truong, Sandra K., Sreedasyam, Avinash, Jenkins, Jerry, Shu, Shengqiang, Sims, David, Kennedy, Megan, Amirebrahimi, Mojgan, Weers, Brock D., McKinley, Brian, Mattison, Ashley, Morishige, Daryl T., Grimwood, Jane, Schmutz, Jeremy, and Mullet, John E. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. United States: N. p., 2017. Web. doi:10.1111/tpj.13781.
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McCormick, Ryan F., Truong, Sandra K., Sreedasyam, Avinash, Jenkins, Jerry, Shu, Shengqiang, Sims, David, Kennedy, Megan, Amirebrahimi, Mojgan, Weers, Brock D., McKinley, Brian, Mattison, Ashley, Morishige, Daryl T., Grimwood, Jane, Schmutz, Jeremy, & Mullet, John E. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. United States. https://doi.org/10.1111/tpj.13781
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McCormick, Ryan F., Truong, Sandra K., Sreedasyam, Avinash, Jenkins, Jerry, Shu, Shengqiang, Sims, David, Kennedy, Megan, Amirebrahimi, Mojgan, Weers, Brock D., McKinley, Brian, Mattison, Ashley, Morishige, Daryl T., Grimwood, Jane, Schmutz, Jeremy, and Mullet, John E. Tue . "The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization". United States. https://doi.org/10.1111/tpj.13781. https://www.osti.gov/servlets/purl/1616057.
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@article{osti_1616057,
title = {The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization},
author = {McCormick, Ryan F. and Truong, Sandra K. and Sreedasyam, Avinash and Jenkins, Jerry and Shu, Shengqiang and Sims, David and Kennedy, Megan and Amirebrahimi, Mojgan and Weers, Brock D. and McKinley, Brian and Mattison, Ashley and Morishige, Daryl T. and Grimwood, Jane and Schmutz, Jeremy and Mullet, John E.},
abstractNote = {Summary Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 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. Subtelomeric 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 more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms ( SNP s) and 1.9 M indels. Large‐scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA ‐seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and 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.},
doi = {10.1111/tpj.13781},
journal = {The Plant Journal},
number = 2,
volume = 93,
place = {United States},
year = {Tue Nov 21 00:00:00 EST 2017},
month = {Tue Nov 21 00:00:00 EST 2017}
}
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https://doi.org/10.1111/tpj.13781
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