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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #394645

Research Project: Development of Economically Important Row Crops that Improve the Resilience of U.S. Agricultural Production to Present and Future Production Challenges

Location: Plant Stress and Germplasm Development Research

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

item CHAVEZ-MONTES, RICARDO - Texas Tech University
item Ulloa, Mauricio
item ZACKAY, ARIK - Nrgene
item KFIR, NIR - Nrgene
item LOPEZ-ARRENDONDO, DAMAR - Texas Tech University
item HERRERA-ESTRELLA, LUIS - Texas Tech University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/28/2022
Publication Date: 1/15/2023
Citation: Chavez-Montes, R., Ulloa, M., Biniashvili, T., Zackay, A., Kfir, N., Lopez-Arrendondo, 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. Article 11.

Interpretive Summary: Pima cotton has long been recognized for its superior fiber quality and premium textile characteristics, compared to Upland cotton. Despite the superiority of Pima fiber quality, it makes up less than 10% of world production. Recently, Pima has proved to be a valuable source of genetic resistance to Fusarium wilt race 4 (FOV4). As such, interest in Pima genetics has increased. In this study, ARS scientists and university cooperators describe the whole genome sequence of Pima-S6. The information in this study describes the genome sequence of Pima-S6, including the assembly of cotton chromosomes and identification of gene functions. These results represent a significant contribution in Pima cotton genetic research and will facilitate the work of identifying and manipulating important genes/traits such as FOV4 resistance and fiber quality improvement, assisting in the processes of future breeding programs.

Technical 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. barbadense 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.