Improved chromosome genome assembly, structural variation insight, and annotation of Gossypium barbadense L. 'Pima-S6'

Abstract Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market. We report a high-quality genome assembly and annotation of Pima-S6 cotton and its comparison at the chromosome and protein level to other ten Gossypium published genome-assemblies. The analyses revealed important differences on structural variations and annotated proteins between our Pima-S6 and other publicly available G. barbadense assemblies, and across Gossypium assemblies in general. Detailed synteny analyses reveals chromosomal rearrangements between Pima-S6 and other Gossypium genomes on several chromosomes. Analyses of the re-assembled and re-annotated genome of the close relative G. barbadenses Pima 3–74 using our Pima-S6 assembly, suggest that contig placement of the most recent G. barbadense assemblies might have been unduly influenced by the use of the G. hirsutum TM-1 genome as the anchoring reference. The Pima-S6 reference genome provides a valuable genomic resource and offers new insights of genomic structure and can serve as G. barbadense genome reference for future assemblies and further support FOV4-related studies and breeding efforts.