High quality genome assembly of Pima-S6 (Gossypium barbadense L) and its insight composition

Authors: Ulloa, Mauricio; LOPEZ-ARREDONDO, DAMAR - Texas Tech University; CHAVEZ-MONTES, RICARDO - Texas Tech University; Payton, Paxton; HERRERA-ESTRELLA, LUIS - Texas Tech University

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 5/5/2022
Publication Date: 1/27/2023
Citation: Ulloa, M., Lopez-Arredondo, D., Chavez-Montes, R., Payton, P.R., Herrera-Estrella, L. 2023. High quality genome assembly of Pima-S6 (Gossypium barbadense L) and its insight composition. National Center for Biotechnology Information (NCBI) BioProject accession PRJNA798371.

Interpretive Summary: Gossypium barbadense also known as Pima cotton is widely recognized for producing premium cotton fibers. Another unique trait of Pima cotton is its resistance to the fungal pathogen responsible for a deadly wilting disease called Fusarium wilt. While Pima cotton is grown under smaller acreages as a niche cotton crop, Gossypium hirsutum or Upland cotton, is grown under a much wider range of environments and accounts for the majority of US cotton fiber. To date, there is no known resistance in Upland cotton to Fusarium wilt. Recently, Fusarium wilt was identified in Texas, the largest producer of Upland cotton, and is a threat to Upland production and the economic base of large rural areas of the Texas. This project was focused on identifying genetic factors in Pima that are associated with disease resistance with the goal of identifying and transferring those factors to Upland cotton to improve disease tolerance. This sequence data is deposited in a public database as a tool for the cotton research community and provides a new valuable genetic resource and for improving disease resistance in Upland cotton through breeding.

Technical Abstract: Gossypium barbadense also known as Pima cotton and widely recognized for producing high-premium value of superior fibers and for Fusarium wilt race 4 (FOV4) resistance remains largely unexplored at the genomic and molecular level. A novel high-quality genome assembly was performed of Pima-S6. DNA isolation targeted high-molecular weight (HMW)-DNA extraction from isolated nuclei which was used to generate three libraries (160X, 52X, and 82X). The genome was sequenced using paired-end and mate-pair libraries short reads sequencing with additional linked-reads sequencing libraries (10X genomics™ Chromium™) and the genome assembly was conducted using the DeNovoMAGICTM software platform (NRGene, Nes Ziona, Isreal). A 2,301,422,177 bp assembly was obtained, with 26 pseudo-chromosomes totaling 2,244,350,239 bp. Pima-S6 assembly revealed a better BUSCO score of completeness (> 97%) for the At and Dt subgenomes than previously published Pima genomes. A comparative analysis at the chromosome and protein level with other 10 Gossypium published genomes detected important structural variations (synteny, inversions, translocations, and duplications) and differences on annotated proteins with other published G. barbadense and across Gossypium assemblies. Synteny analyses validated the chromosomal rearrangements in several chromosomes between Pima-S6 and Upland (G. hirsutum L) TM-1. The final 2.3 Gb Pima-S6 assembly annotated using MAKER-P predicted 88,343 genes of which more than 75,000 genes revealed evidence of homology to known proteins and 1,965 genes evidence of expression in an RNA-seq dataset obtained from roots and leaves of Pima-S6 plants. Comparisons of Pima-S6 assembly at the chromosome and gene sequence-level to other Gossypium species suggest that the results are highly influenced by the methodologies and strategies used to sequence/assemble the genome and to annotate proteins. The Pima-S6 genome provides a new valuable genomic resource and will help us to identify/dissect genes related to important traits such as FOV4 resistance and fiber quality improvement, assisting in the processes of future breeding programs.