Sorghum bicolor ssp. bicolor PI561072 Assembly and Gene Annotation

About Genus species

Germplasm synonyms: * GRIN: PI 561072

IPR

Crop Science Registration. PL-235, SORGHUM. Issued: 01 Nov 1992. * Miller, F. R., C. Domanski, & L. M. Giorda. 1992. A/BTxARG-1 Sorghum Parental Line. Crop Sci. (Madison) 32(6):1517. Note: PL-235

Assembly

The preliminary assembly was constructed using Hifiasm* (v0.19.8) using ~50x coverage of HiFi long reads (Q>20) from a PacBio Revio platform. Resulting contigs were scaffolded using the RagTag* program (v2.1.0) against the BTx623 v5 genome. The resulting assembly was assessed for completeness and quality with the BUSCO* and QUAST*. Contiguity and synteny to BTx623 v5 was checked using the D-Genies dot plot program (https://dgenies.toulouse.inrae.fr/)*.

Annotation

Gene annotations were built by the Ware Lab in CSHL using a pan-gene index from reference gene models and propagated to representative assemblies using the Liftoff tool and further updating their structure using PASA tool.

Regulation

Variation

Sorghum BTx623 (NCBIv3): 47 million rsIDs provided from European Variation Archive SNPs were assigned using the variant-remapping pipeline from EBI.

References

• Cheng, H., Jarvis, E.D., Fedrigo, O., Koepfli, K.P., Urban, L., Gemmell, N.J., Li, H. (2022) Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology, 40:1332–1335. https://doi.org/10.1038/s41587-022-01261-x
• Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17.
• Mosè Manni, Matthew R Berkeley, Mathieu Seppey, Felipe A Simão, Evgeny M Zdobnov, BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution, Volume 38, Issue 10, October 2021, Pages 4647–4654
• https://pubmed.ncbi.nlm.nih.gov/23422339/
• Cabanettes F, Klopp C. (2018) D-GENIES: dot plot large genomes in an interactive, efficient and simple way. PeerJ 6:e4958 https://doi.org/10.7717/peerj.4958

Links

More information

General information about this species can be found in Wikipedia.