Sb bicolor IS929 Assembly and Gene Annotation

About Sorghum IS929

IS929 is a landrace of Sorghum bicolor collected in Sudan. Its name is Hegari Mackwar and alternate identifiers are PI 568989 (USDA), FC 4606, HSD 7858 and SU 10. It is considered to belong to the durra race. It was re-sequenced to broaden the sampling of the durra race.

Assembly

The genome assembly of Sorghum IS929 was reported in Tao et al, 2021. Sequencing was conducted by the Australia Sorghum breeding team in collaboration with BGI-Shenzhen using Illumina HiSeq 4000 platform and the PacBio Sequel platform to achieve 176X and 46X coverage, respectively. The assembly effort generated a genome of 580Mb with contigs N50 of 342kb.

Annotation

Gene prediction was performed using a hybrid approach combining de novo gene predictors and evidence-based methods, which led to the identification of 35,889 genes in the genome.

References

Literatures, publications related to this genome and data

1. Extensive variation within the pan-genome of cultivated and wild sorghum.Tao Y, Luo H, Xu J, Cruickshank A, Zhao X, Teng F, Hathorn A. Wu X. Liu Y. Shatte T et al. Nat. Plants.
2. The Sorghum bicolor genome and the diversification of grasses. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al. 2009. Nature. 457:551-556.
3. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. McCormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers BD, McKinley B et al. 2018. Plant J. 93:338-354.
4. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE et al. 2013. Proc. Natl. Acad. Sci. U.S.A.. 110:453-458.
5. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X et al. 2013. Nat Commun. 4:2320.
6. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z. 2016. Plant Cell. 28:1551-1562.
7. Applying genotyping (TILLING) and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population. Xin Z, Wang ML, Barkley NA, Burow G, Franks C, Pederson G, Burke J. 2008. BMC Plant Biol 2008, 8:103.
8. Forward Genetics by Sequencing EMS Variation-Induced Inbred Lines. Addo-Quaye C, Buescher E, Best N, Chaikam V, Baxter I and Dilkes BP. 2017. G3: Genes, Genomes, Genetics. 7(2):413-425.

Links

1. USDA - https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1463960
2. ICRISAT - http://genebank.icrisat.org/IND/PassportSummary?ID=IS%20929
3. FAO - https://ssl.fao.org/glis/doi/10.18730/N2SKM

   More information

General information about this species can be found in Wikipedia.

More information

General information about this species can be found in Wikipedia.