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Sorghum purpureosericeum PI536008 C048 Assembly and Gene Annotation

About Sorghum PI536008

PI536008 is a wild Sorghum accession from near Waza (11.2500, 14.6667), Maroua, Extreme-Nord Province in Cameroon. It is classified in GRIN as S.purpureosericeum. One botanist (Bryan Simon) at the Queensland Herbarium questioned this classification, contending it is more likely S.bicolor. PI536008 appears to be fully interfertile with cultivated sorghum and it has been used as a CWR parent in both the Queensland core pre-breeding program and the sorghum CWR BCNAM panel supported by the Global Crop Diversity Trust. Prior to its donation to the USDA collection, it was designated TCD070 by IBPGR.

Assembly

The genome assembly of Sorghum PI536008 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 192X and 58X coverage, respectively. The assembly effort generated a genome of 672.5Mb with contigs N50 of 185.1kb.

Annotation

Gene prediction was performed using a hybrid approach combining de novo gene predictors and evidence-based methods (Tao et al, 2021), which led to the identification of 33,227 genes in the genome.

References

  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.

USDA https://npgsweb.ars-grin.gov/gringlobal/accessiondetail?id=1430944

More information

General information about this species can be found in Wikipedia.

More information

General information about this species can be found in Wikipedia.

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