skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Authors:
 [1];  [1];  [2];  [2];  [3];  [2];  [3];  [3];  [4];  [4];  [1];  [4];  [5];  [5];  [4]
  1. Interdisciplinary Program in Genetics Texas A&,M University College Station TX 77843 USA, Department of Biochemistry and Biophysics Texas A&,M University College Station TX 77843 USA
  2. HudsonAlpha Institute for Biotechnology Huntsville AL 35806 USA
  3. Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
  4. Department of Biochemistry and Biophysics Texas A&,M University College Station TX 77843 USA
  5. HudsonAlpha Institute for Biotechnology Huntsville AL 35806 USA, Department of Energy Joint Genome Institute Walnut Creek CA 94598 USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1415049
Grant/Contract Number:  
DE‐FC02‐07ER64494; DE‐AC02‐05CH11231; DE‐AR0000596; DE‐SC0012629
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Name: The Plant Journal Journal Volume: 93 Journal Issue: 2; Journal ID: ISSN 0960-7412
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English

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 Kingdom: N. p., 2017. Web. doi:10.1111/tpj.13781.
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 Kingdom. doi:10.1111/tpj.13781.
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. Sat . "The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization". United Kingdom. doi:10.1111/tpj.13781.
@article{osti_1415049,
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 = {},
doi = {10.1111/tpj.13781},
journal = {The Plant Journal},
number = 2,
volume = 93,
place = {United Kingdom},
year = {2017},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1111/tpj.13781

Citation Metrics:
Cited by: 20 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Distribution and sequence analysis of the centromere-associated repetitive element CEN38 of Sorghum bicolor (Poaceae)
journal, December 2000

  • Zwick, M. S.; Islam-Faridi, M. N.; Zhang, H. B.
  • American Journal of Botany, Vol. 87, Issue 12
  • DOI: 10.2307/2656825

The Sorghum bicolor genome and the diversification of grasses
journal, January 2009

  • Paterson, Andrew H.; Bowers, John E.; Bruggmann, Rémy
  • Nature, Vol. 457, Issue 7229
  • DOI: 10.1038/nature07723

Insights into the Maize Pan-Genome and Pan-Transcriptome
journal, January 2014

  • Hirsch, Candice N.; Foerster, Jillian M.; Johnson, James M.
  • The Plant Cell, Vol. 26, Issue 1
  • DOI: 10.1105/tpc.113.119982

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability
journal, March 2015

  • Mickelbart, Michael V.; Hasegawa, Paul M.; Bailey-Serres, Julia
  • Nature Reviews Genetics, Vol. 16, Issue 4
  • DOI: 10.1038/nrg3901

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)
journal, January 2011


From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
journal, October 2013

  • Auwera, Geraldine A.; Carneiro, Mauricio O.; Hartl, Christopher
  • Current Protocols in Bioinformatics, Vol. 43, Issue 1
  • DOI: 10.1002/0471250953.bi1110s43

Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development of Sorghum bicolor
journal, September 2016

  • McKinley, Brian; Rooney, William; Wilkerson, Curtis
  • The Plant Journal, Vol. 88, Issue 4
  • DOI: 10.1111/tpj.13269

Moderation of Arabidopsis Root Stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 Receptor Kinase Complexes
journal, March 2013


Chromosome Identification and Nomenclature of Sorghum bicolor
journal, October 2004


Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009


Determinants of nucleosome positioning and their influence on plant gene expression
journal, June 2015

  • Liu, Ming-Jung; Seddon, Alexander E.; Tsai, Zing Tsung-Yeh
  • Genome Research, Vol. 25, Issue 8
  • DOI: 10.1101/gr.188680.114

The Influence of Recombination on Human Genetic Diversity
journal, January 2006


mreps: efficient and flexible detection of tandem repeats in DNA
journal, July 2003


Plant Genome Engineering with Sequence-Specific Nucleases
journal, April 2013


Combined Evidence Annotation of Transposable Elements in Genome Sequences
journal, January 2005


A survey of the sorghum transcriptome using single-molecule long reads
journal, June 2016

  • Abdel-Ghany, Salah E.; Hamilton, Michael; Jacobi, Jennifer L.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms11706

Expanding and Vetting Gene Annotations through Transcriptome and Methylome Sequencing
journal, January 2014


Considering Transposable Element Diversification in De Novo Annotation Approaches
journal, January 2011


Genome Evolution in the Genus Sorghum (Poaceae)
journal, January 2005


A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy
journal, June 2016


Repbase Update, a database of repetitive elements in eukaryotic genomes
journal, June 2015


Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
journal, November 2015

  • VanBuren, Robert; Bryant, Doug; Edger, Patrick P.
  • Nature, Vol. 527, Issue 7579
  • DOI: 10.1038/nature15714

GtRNAdb: a database of transfer RNA genes detected in genomic sequence
journal, January 2009

  • Chan, P. P.; Lowe, T. M.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn787

Resolution of Genetic Map Expansion Caused by Excess Heterozygosity in Plant Recombinant Inbred Populations
journal, August 2014

  • Truong, Sandra K.; McCormick, Ryan F.; Morishige, Daryl T.
  • G3: Genes|Genomes|Genetics, Vol. 4, Issue 10
  • DOI: 10.1534/g3.114.012468

Impact of chromatin structure on sequence variability in the human genome
journal, March 2011

  • Tolstorukov, Michael Y.; Volfovsky, Natalia; Stephens, Robert M.
  • Nature Structural & Molecular Biology, Vol. 18, Issue 4
  • DOI: 10.1038/nsmb.2012

Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes
journal, November 2001

  • Witte, C. -P.; Le, Q. H.; Bureau, T.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 24
  • DOI: 10.1073/pnas.241341898

Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function
journal, August 2014


Identification of Dw1, a Regulator of Sorghum Stem Internode Length
journal, March 2016


Redesigning photosynthesis to sustainably meet global food and bioenergy demand
journal, June 2015

  • Ort, Donald R.; Merchant, Sabeeha S.; Alric, Jean
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 28
  • DOI: 10.1073/pnas.1424031112

Compilation and Characterization of a Novel WNK Family of Protein Kinases in Arabiodpsis thaliana with Reference to Circadian Rhythms
journal, January 2002

  • Nakamichi, Norihito; Murakami-Kojima, Masaya; Sato, Eriko
  • Bioscience, Biotechnology, and Biochemistry, Vol. 66, Issue 11
  • DOI: 10.1271/bbb.66.2429

RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK
journal, February 2015

  • McCormick, Ryan F.; Truong, Sandra K.; Mullet, John E.
  • G3: Genes|Genomes|Genetics, Vol. 5, Issue 4
  • DOI: 10.1534/g3.115.017012

Transcriptome Profiling of Tiller Buds Provides New Insights into PhyB Regulation of Tillering and Indeterminate Growth in Sorghum
journal, February 2016

  • Kebrom, Tesfamichael H.; Mullet, John E.
  • Plant Physiology, Vol. 170, Issue 4
  • DOI: 10.1104/pp.16.00014

Improving photosynthesis and crop productivity by accelerating recovery from photoprotection
journal, November 2016

  • Kromdijk, Johannes; Głowacka, Katarzyna; Leonelli, Lauriebeth
  • Science, Vol. 354, Issue 6314
  • DOI: 10.1126/science.aai8878

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
journal, October 2011


A dynamic gene expression atlas covering the entire life cycle of rice
journal, March 2010


Genome-wide atlas of transcription during maize development
journal, March 2011


A framework for variation discovery and genotyping using next-generation DNA sequencing data
journal, April 2011

  • DePristo, Mark A.; Banks, Eric; Poplin, Ryan
  • Nature Genetics, Vol. 43, Issue 5
  • DOI: 10.1038/ng.806

Energy Sorghum--a genetic model for the design of C4 grass bioenergy crops
journal, June 2014

  • Mullet, J.; Morishige, D.; McCormick, R.
  • Journal of Experimental Botany, Vol. 65, Issue 13
  • DOI: 10.1093/jxb/eru229

Predicting Human Nucleosome Occupancy from Primary Sequence
journal, August 2008


Rapid method for high-quality RNA isolation from seed endosperm containing high levels of starch
journal, June 2005


Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
journal, January 2016


Genetic hitchhiking
journal, November 2000

  • Barton, N. H.
  • Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Vol. 355, Issue 1403
  • DOI: 10.1098/rstb.2000.0716

The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
journal, January 2004


Genome-Wide Prediction of Nucleosome Occupancy in Maize Reveals Plant Chromatin Structural Features at Genes and Other Elements at Multiple Scales
journal, April 2013

  • Fincher, Justin A.; Vera, Daniel L.; Hughes, Diana D.
  • Plant Physiology, Vol. 162, Issue 2
  • DOI: 10.1104/pp.113.216432

A bouquet of chromosomes
journal, August 2004


Population genomic and genome-wide association studies of agroclimatic traits in sorghum
journal, December 2012

  • Morris, G. P.; Ramu, P.; Deshpande, S. P.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 2
  • DOI: 10.1073/pnas.1215985110

Stable inheritance of telomere chromatin structure and function in the absence of telomeric repeats
journal, September 2003


Agrochemical control of plant water use using engineered abscisic acid receptors
journal, February 2015

  • Park, Sang-Youl; Peterson, Francis C.; Mosquna, Assaf
  • Nature, Vol. 520, Issue 7548
  • DOI: 10.1038/nature14123

ENCODE Data in the UCSC Genome Browser: year 5 update
journal, November 2012

  • Rosenbloom, Kate R.; Sloan, Cricket A.; Malladi, Venkat S.
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1172

Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites
journal, January 2009


Organization and function of the 3D genome
journal, October 2016

  • Bonev, Boyan; Cavalli, Giacomo
  • Nature Reviews Genetics, Vol. 17, Issue 11
  • DOI: 10.1038/nrg.2016.112

Variation in the mutation rate across mammalian genomes
journal, October 2011

  • Hodgkinson, Alan; Eyre-Walker, Adam
  • Nature Reviews Genetics, Vol. 12, Issue 11
  • DOI: 10.1038/nrg3098

The effects of chromatin organization on variation in mutation rates in the genome
journal, March 2015

  • Makova, Kateryna D.; Hardison, Ross C.
  • Nature Reviews Genetics, Vol. 16, Issue 4
  • DOI: 10.1038/nrg3890

Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays
journal, April 2013


YASS: enhancing the sensitivity of DNA similarity search
journal, July 2005

  • Noe, L.; Kucherov, G.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki478

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
journal, July 2010


The plant WNK gene family and regulation of flowering time in Arabidopsis
journal, September 2008


Reference genome sequence of the model plant Setaria
journal, May 2012

  • Bennetzen, Jeffrey L.; Schmutz, Jeremy; Wang, Hao
  • Nature Biotechnology, Vol. 30, Issue 6
  • DOI: 10.1038/nbt.2196

Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum
journal, September 2011

  • Murphy, R. L.; Klein, R. R.; Morishige, D. T.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 39, p. 16469-16474
  • DOI: 10.1073/pnas.1106212108

Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation
journal, June 2015


Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential
journal, May 2012

  • Zhang, Gengyun; Liu, Xin; Quan, Zhiwu
  • Nature Biotechnology, Vol. 30, Issue 6
  • DOI: 10.1038/nbt.2195

Multiple sequence alignment with hierarchical clustering
journal, November 1988


Analysis of the bread wheat genome using whole-genome shotgun sequencing
journal, November 2012

  • Brenchley, Rachel; Spannagl, Manuel; Pfeifer, Matthias
  • Nature, Vol. 491, Issue 7426
  • DOI: 10.1038/nature11650

Registration of the BTx623/IS3620C Recombinant Inbred Mapping Population of Sorghum
journal, January 2011


The protein kinase TOUSLED facilitates RNAi in Arabidopsis
journal, June 2014

  • Uddin, Mohammad Nazim; Dunoyer, Patrice; Schott, Gregory
  • Nucleic Acids Research, Vol. 42, Issue 12
  • DOI: 10.1093/nar/gku422

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
journal, October 2015

  • Sanborn, Adrian L.; Rao, Suhas S. P.; Huang, Su-Chen
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 47
  • DOI: 10.1073/pnas.1518552112

The B73 Maize Genome: Complexity, Diversity, and Dynamics
journal, November 2009

  • Schnable, P. S.; Ware, D.; Fulton, R. S.
  • Science, Vol. 326, Issue 5956, p. 1112-1115
  • DOI: 10.1126/science.1178534

Repeat DNA in genome organization and stability
journal, April 2015

  • Padeken, Jan; Zeller, Peter; Gasser, Susan M.
  • Current Opinion in Genetics & Development, Vol. 31
  • DOI: 10.1016/j.gde.2015.03.009

Digital genotyping of sorghum -- a diverse plant species with a large repeat-rich genome
journal, January 2013

  • Morishige, Daryl T.; Klein, Patricia E.; Hilley, Josie L.
  • BMC Genomics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2164-14-448

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum
journal, August 2013

  • Mace, Emma S.; Tai, Shuaishuai; Gilding, Edward K.
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3320

Regulation of floral patterning and organ identity by Arabidopsis ERECTA-family receptor kinase genes
journal, September 2013

  • Bemis, Shannon M.; Lee, Jin Suk; Shpak, Elena D.
  • Journal of Experimental Botany, Vol. 64, Issue 17
  • DOI: 10.1093/jxb/ert270

Extensive Variation in the Density and Distribution of DNA Polymorphism in Sorghum Genomes
journal, November 2013