Sb bicolor PI154987 Assembly and Gene Annotation

About Sorghum PI154987

Sorghum (Sorghum bicolor [L.] Moench) is a drought-tolerant, warm-season C4 grass cultivated globally for grain, forage, and bioenergy applications. It is a flagship species for genomic research due to its relatively small, diploid genome and extensive germplasm resources.

The PI_154987 accession is one of 32 diverse sorghum lines selected for de novo genome assembly as part of the Sorghum pan-genome project. This line contributes to capturing global genetic diversity and supports investigations into presence–absence variation, copy number variation, and structural genomic diversity relevant to agronomic and bioenergy traits.

Assembly

The Sorghum bicolor PI_154987 genome was assembled using long-read PacBio sequencing data and polished using RACON. Assembly refinement included correction of misjoins, chromosome scaffolding using syntenic markers, and haplotype collapsing. Final assemblies consist of 10 chromosomes and were screened for contaminants and corrected using Illumina short reads.

Annotation

Gene annotation for Sorghum bicolor PI_154987 was performed as part of a two-round pan-genome annotation strategy.

In the first round, transcript assemblies derived from Illumina RNA-seq data were generated using PERTRAN and PASA. Homology-based gene prediction methods included FGENESH, FGENESH_EST, EXONERATE, AUGUSTUS, and PASA-derived ORFs. Predictions were filtered based on transcript support, protein homology, repeat overlap, and domain composition.

In the second round, high-confidence gene models were propagated across the pan-genome using homology-based predictions from other sorghum genomes. Low-confidence, repetitive, or weakly supported models were removed to generate a refined gene set.

Regulation

Variation

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

References

Key references supporting the Sorghum pan-genome project include:

• Paterson et al. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature.
• Hickey et al. (2020). Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biology.
• Song et al. (2022). AnchorWave: sensitive alignment of genomes with high sequence diversity. PNAS.
• Li et al. (2022). Plant pan-genomics: recent advances, new challenges, and roads ahead. Journal of Genetics and Genomics.

Links

More information

General information about this species can be found in Wikipedia.