Assembly and annotation of the Gossypium barbadense L. ‘Pima-S6’ genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes

Abstract

Background: 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. Results: Synteny and orthogroup analyses revealed important differences on chromosome structure and annotated proteins content between our Pima-S6 and other publicly available G. barbadense assemblies, and across Gossypium assemblies in general. Detailed synteny analyses revealed chromosomal rearrangements between Pima-S6 and other Pima genomes on several chromosomes, with three major inversions in chromosomes A09, A13 and D05, raising questions about the true chromosome structure of Gossypium barbadense genomes. Conclusion: Analyses of the re-assembled and re-annotated genome of the close relative G. barbadense Pima 3–79 using our Pima-S6 assembly suggest that contig placement of some 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 on genomic structure, and can serve as G. barbadense genome reference for future assemblies and further support FOV4-related studies and breeding efforts.

Description

© 2023, The Author(s). cc-by

Keywords

Comparative genomics, Cotton genome, Genome assembly, Pima cotton

Citation

Chavez, Montes, R.A., Ulloa, M., Biniashvili, T., Zackay, A., Kfir, N., Lopez-Arredondo, D., & Herrera-Estrella, L.. 2023. Assembly and annotation of the Gossypium barbadense L. ‘Pima-S6’ genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes. BMC Genomics, 24(1). https://doi.org/10.1186/s12864-022-09102-6

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