Sb bicolor chinese amber Assembly and Gene Annotation

About Chinese Amber [PI 22913]

Chinese Amber was one of the first commercially produced sorghum lines ever introduced into the U.S. in 1853. It is a historically sweet sorghum that is primarily used for syrup production rather than sucrose extraction. It is also one of the more genetically distinct sorghum varieties that can be used for biofuel production, which is why it was selected as one of the parents for the CP-NAM population (Boatwright et al, 2021).

Germplasm synonyms: * GRIN: PI 22913 * ICRISAT: IS 12711, IS 605

Population panels: * Sorghum Bioenergy Association Panel (BAP) - 386 accessions (Brenton et al, 2016) * CP-NAM - 12 accessions (Boatwright et al, 2021; Boatwright et al, 2022; Kumar et al, 2022)

Assembly

The preliminary assembly was constructed using Canu and 30x coverage Pacbio long read data and then aligned to the reference (BTx623) using MUMmer (Voelker et al, 2022). Contigs were sorted using coordinate data from MUMmer and code developed by the Cooper Lab at UNCC (https://github.com/cponce-uncc/bioinformatics_tools). Contigs under 50k base pairs were discarded, as were contigs that were manually determined to not clearly map to a position after sorting. Final assembly statistics are as follows:

Final Contig Count: 628

Final Base Pair Count: 634688368

Percent Coverage of Reference: 86.944%

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 (Voelker et al, 2022).

References

Boatwright JL, Brenton ZW, Boyles RE, Sapkota S, Myers MT, Jordan KE, Dale SM, Shakoor N, Cooper EA, Morris GP, Kresovich S. 2021. Genetic characterization of a Sorghum bicolor multiparent mapping population emphasizing carbon-partitioning dynamics. G3 (Bethesda). 11(4):jkab060. PMID: 33681979. doi: 10.1093/g3journal/jkab060.

Boatwright JL, Sapkota S, Jin H, Schnable JC, Brenton Z, Boyles R, Kresovich S. 2022. Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity. Plant J. PMID: 35653240. doi: 10.1111/tpj.15853.

Kumar N, Brenton ZW, Myers MT, Boyles RE, Sapkota S, Boatwright JL, Cox WA, Jordan KE, Kresovich S. 2022. Registration of the sorghum carbon‐partitioning nested association mapping (CP‐NAM) population. Journal of Plant Registrations. 1-8. doi: 10.1002/plr2.20229.

Voelker WG, Krishnan K, Chougule K, Alexander LC, Lu Z, Olson A, Ware W, Songsomboon K, Ponce C, Brenton ZW, Boatwright JL, Cooper EA. 2022. Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes. bioRxiv. doi: 10.1101/2022.09.26.509520.

Links

• GRIN: PI 22913
• Germplasm page at Genbank ICRISAT: IS 12711
• Passport summary at ICRISAT: IS 12711
• Passport summary at FAO: 10.18730/NBZN*
• Passport data at Genesys: 10.18730/NBZN*