Sb bicolor PI655972 pink kafir Assembly and Gene Annotation

About PI 655972

Also known as “Pink Kafir,” PI 655972 is a tall sorghum genotype that has been used for grain as well as fodder for livestock. It is one of the parents in the CP-NAM population (Boatwright et al. 2021).

Germplasm synonyms: * GRIN: PI 655972 * ICRISAT: IS 200 * Cultivar: PINK KAFIR * SAP: SAP-95

Population panels: * Sorghum Association Panel (SAP) - 407 accessions (Casa et al, 2008) * 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 42x 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: 867

Final Base Pair Count: 661782914

Percent Coverage of Reference: 90.655%

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 655972