Sb bicolor PI601264 PH227 Assembly and Gene Annotation
About PI 601264
Sorghum bicolor, a diploid cereal crop with a genome size of approximately 730 Mb and 10 haploid chromosomes, is the fifth most produced cereal worldwide (Paterson et al., 2009). Primarily cultivated in Africa, sorghum is also recognized for its potential as a biofuel crop and a source of cellulosic feedstock (George et al., 2022). Its relatively compact genome makes sorghum an excellent model for functional genomics studies of Saccharinae and other C4 grasses.
In the United States, Plant Variety Protection (PVP) laws safeguard inbred sorghum lines developed by private companies for 20 years. After this period, these lines, known as ex-PVPs, become publicly accessible, providing valuable genetic resources for breeding programs aimed at enhancing yield, disease resistance, and climate resilience
Plant material: Seeds were obtained from the USDA Germplasm Information Resource Network (GRIN)
Germplasm synonyms: * GRIN: PI 601264
IPR
U.S. Plant Variety Protection
PVP 8600012
Variety: PH227
Taxonomy: Sorghum bicolor (L.) Moench subsp. bicolor
Experimental name/synonym: PH227
Crop: SORGHUM
Applicant: Pioneer Hi-Bred International, Inc.
Date filed: 10/25/1985
Date issued: 04/29/1988
Status: Certificate Expired
Status date: 04/29/2006
Assembly
DNA extraction, sequencing and assembly: High molecular weight (HMW) DNA from young-fresh leaves were extracted and used for long reads using Oxford Nanopore Technologies (ONT) ligation-based libraries (SQK-LSK109). Final libraries were loaded on an ONT flowcell (v9.4.1) and run on the PromethION. Illumina 2x150 paired-end reads were also generated for polishing genome assemblies. Short reads libraries were prepared from HMW DNA using Illumina NexteraXT library prep kit, and sequenced on NextSeq High Output 300 cycle, paired end 2X150 kit (Illumina, San Diego, CA). ONT reads were assembled using Flye (v2.9.2) then polished using Racon (v1.5.0) and Pilon (v1.24) with Illumina reads. Ragtag (v2.1.0) was used to scaffold the contigs. The completeness of the genome assembly was assessed through BUSCO (v. 5.4.3).
Annotation
Using a pan-gene index from reference gene models, pan-genes were propagated to ex-PVP assemblies using the Liftoff tool and made available as tracks on the browser page.
Regulation
Variation
Sorghum BTx623 (NCBIv3): 47 million rsIDs provided from European Variation Archive SNPs were assigned to each ex-PVP assemblies using the variant-remapping pipeline from EBI.
References
Paterson, Andrew H., John E. Bowers, Rémy Bruggmann, Inna Dubchak, Jane Grimwood, Heidrun Gundlach, Georg Haberer, et al. 2009. “The Sorghum Bicolor Genome and the Diversification of Grasses.” Nature 457 (7229): 551–56.
George, Toyosi T., Anthony O. Obilana, Ayodeji B. Oyenihi, Anthony B. Obilana, Damilola O. Akamo, and Joseph M. Awika. 2022. “Trends and Progress in Sorghum Research over Two Decades, and Implications for Global Food Security.” South African Journal of Botany: Official Journal of the South African Association of Botanists = Suid-Afrikaanse Tydskrif Vir Plantkunde: Amptelike Tydskrif van Die Suid-Afrikaanse Genootskap van Plantkundiges 151 (December): 960–69.
Links
More information
General information about this species can be found in Wikipedia.
