Sorghum bicolor (L.) Moench subsp. bicolor, is a widely grown cereal crop, particularly in Africa, ranking 5th in global cereal production (FAOSTAT 2008; http://www.fao.org/in-action/inpho/crop-compendium/cereals-grains/). It is a C4 grass also used for sugar production, brewing, feedstock, and as a biofuel crop. Its diploid genome (~730 Mbp) has a haploid chromosome number of 10. The inbred variety ‘BTx623’ is the current reference genome for sorghum. It has short stature and an early maturing genotype used primarily to produce grain sorghum hybrids. It is a line susceptible to sugarcane aphid and sensitive to low nitrogen, and therefore often used in functional comparative studies.
Germplasm
Plant Introduction (PI) number for Sorghum bicolor (L.) Moench subsp. bicolor, ‘BTx623’ in the U.S. National Plant Germplasm System (GRIN – Global): PI 564163.
This accession is part of the following population panels:
- Sorghum Association Panel (SAP) – 407 accessions (Casa et al, 2008)
- Sorghum Bioenergy Association Panel (BAP) – 386 accessions (Brenton et al, 2016)
Image
Statistics (Source: NCBI, April 2021)
| Sorghum line | BTx623 | |
| Assembly information | ||
| Assembly name | Sorghum_bicolor_NCBIv3 | |
| Assembly date | Jun 2017 | |
| Assembly accession | GCA_000003195.3 | |
| WGS accession | ABXC00000000 | |
| Assembly provider | ||
| Sequencing description | Sequencing technologies: | Sanger; Illumina |
| Sequencing method | ||
| Genome coverage: | 8x | |
| Assembly description | Assembly methods: | ARACHNE_modified v. 200721016 |
| Construction of pseudomolecules | ||
| Finishing strategy | ||
| NCBI submission | ||
| Publication: | Paterson et al (2009); McCormick et al (2018) | |
| Assembly statistics | ||
| Number of contigs | 2,688 | |
| Total assembly length (Mb) | 732 | |
| Contig N50 (Mb) | 1 | |
| Annotations stats | ||
| Total number of genes | 34,118 | |
| Total number of transcripts | 47,121 | |
| Average gene length | 3,714 | |
| Exons per transcript | 5 |
Assembly
The genome assembly of Sorghum bicolor cv. Moench was published in 2009 (Paterson et al, 2009). The present assembly corresponds to v3.1.1 at the US Department of Energy Joint Genome Institute (JGI) described in (McCormick et al, 2018), and is also known as the NCBIv3 assembly. Sequencing by the JGI’s Community Sequencing Program in collaboration with the Plant Genome Mapping Laboratory at the University of Georgia, followed a whole-genome shotgun strategy reaching 8X coverage with scaffolds -where possible- being assigned to the genetic map. JGI did two additional rounds of improvements. The most recent update of release v3.0 included ~351 Mb of finished sorghum sequence. A total of 349 clones were manually inspected, then finished and validated using a variety of technologies including Sanger, 454 and Illumina. They were integrated into chromosomes by aligning to v1.0 assembly. As a result, 4,426 gaps were closed, and a total of 4.96 Mb of sequence was added to the assembly. Overall contiguity (contig N50) increased by a factor of 5.8X from 204.5 Kb to 1.2 Mb. For more details, see Phytozome.
NCBI accession: GCA_000003195.3.
Annotation
Method
Gene predictions resulted from combining homology-based and ab initio methods with expressed sequences from sorghum, maize and sugarcane, using the JGI annotation pipeline (Goodstein et al, 2012). The SorghumBase browser presents data from the current JGI v3.1.1 release, which comprises the v3.0.1 assembly and v3.1.1 gene set (Feb 2017). Read more at Phytozome.
This is a modern annotation using resources used in the original v1.0 release (Sbi1 assembly and Sbi1.4 gene set) and geneAtlas RNA-seq data. The main genome is in 10 chromosomes with small unmapped pieces, some of which contain annotated genes. The NCBIv3 release (Phytozome v3.1.1) is essentially the same as Phytozome v3.1 except for 82 genes/loci that were inactivated due to 4 scaffolds entirely present in chromosome(s) that were removed.
Repeats were annotated with the Ensembl Genomes repeat feature pipeline (Aken et al, 2016), which uses six classes of repeats loaded from ENA.
Repeats
| Repeat feature | Frequency | Coverage (Mb) | % of the genome covered |
| Low complexity (Dust) features | 685,783 | 29 | 4 |
| RepeatMasker (with RepBase library) | 455,749 | 451 | 62.1 |
| RepeatMasker (with REdat library) | 392,778 | 409 | 56.2 |
| Tandem repeats (TRF) features | 245,654 | 41 | 5.7 |
Nomenclature – Converting Gene IDs
To search for older sorghum gene IDs of the form Sobic.* (MIPS/JGI Sbi1.4), you may want to convert them to SbXXX gene IDs (JGI v2.1) using JGI’s conversion file (password protected). The file provides mapping of Sorghum bicolor from MIPS/JGI Sbi1.4 to v2.1 and higher builds.
Example lines:
Sbi1.4 [Sobic.001G000100] ⇔ v2.1 [Sb01g000200]
#new-locusName old-locusName
Sobic.001G000100 Sb01g000200
#new-transcriptName old-transcriptName
Sobic.001G000100.1 Sb01g000200.1
To convert to the Ensembl nomenclature in use at SorghumBase, the following rule applies:
Sobic.* => SORBI_3*
For example:
Sobic.001G544600 = SORBI_3001G544600
Literature References
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Brenton, Zachary W., Elizabeth A. Cooper, Mathew T. Myers, Richard E. Boyles, Nadia Shakoor, Kelsey J. Zielinski, Bradley L. Rauh, William C. Bridges, Geoffrey P. Morris, and Stephen Kresovich. 2016. “A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy.” Genetics 204 (1): 21–33. PMID: 27356613. https://doi.org/10.1534/genetics.115.183947.
Casa, Alexandra M., Gael Pressoir, Patrick J. Brown, Sharon E. Mitchell, William L. Rooney, Mitchell R. Tuinstra, Cleve D. Franks, and Stephen Kresovich. 2008. “Community Resources and Strategies for Association Mapping in Sorghum.” Crop Science 48 (1): 30–40. https://doi.org/10.2135/cropsci2007.02.0080.
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McCormick, Ryan F., Sandra K. Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, et al. 2018. “The Sorghum Bicolor Reference Genome: Improved Assembly, Gene Annotations, a Transcriptome Atlas, and Signatures of Genome Organization.” The Plant Journal: For Cell and Molecular Biology 93 (2): 338–54. PMID: 29161754. https://doi.org/10.1111/tpj.13781.
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Makita, Yuko, Setsuko Shimada, Mika Kawashima, Tomoko Kondou-Kuriyama, Tetsuro Toyoda, and Minami Matsui. 2015. “MOROKOSHI: Transcriptome Database in Sorghum Bicolor.” Plant & Cell Physiology 56 (1): e6. PMID: 25505007. https://doi.org/10.1093/pcp/pcu187.
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Xin, Zhanguo, Ming Li Wang, Noelle A. Barkley, Gloria Burow, Cleve Franks, Gary Pederson, and John Burke. 2008. “Applying Genotyping (TILLING) and Phenotyping Analyses to Elucidate Gene Function in a Chemically Induced Sorghum Mutant Population.” BMC Plant Biology. PMID: 18854043. https://doi.org/10.1186/1471-2229-8-103.
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