Sorghum bicolor ssp. bicolor PI552861 Assembly and Gene Annotation
About Genus species
Germplasm synonyms: * GRIN: PI 552861
IPR
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.
