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. 2023 Feb 9;13(2):jkac308.
doi: 10.1093/g3journal/jkac308.

The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication

Affiliations

The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication

Thiruvarangan Ramaraj et al. G3 (Bethesda). .

Abstract

Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the 2 domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv.) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv. Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.

Keywords: Gossypium herbaceum; Wagad; cotton; genome sequence.

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Conflict of interest statement

Conflicts of interest The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Plot of Hi–C interaction plots for the A1-Wagad genome. The x- and y-axis both depict a linear representation of the genome from top left (chromosome 1) to bottom right (chromosome 13). The blue boxes on the diagonal represent the chromosomes. The color intensity represents the number of HiC interactions along the chromosome and illustrates that most chromatin interactions are with other nucleotides from the same chromosome.
Fig. 2.
Fig. 2.
a) Genome alignment of the 13 chromosomes in the G. herbaceum var. africanum (y-axis) and the G. herbaceum cv. Wagad (x-axis) genomes. The shade of blue indicates the degree of sequence match. The orange circles indicate major and minor inversions between the 2 genome assemblies on chromosomes A01, A02, A06, and A13. b) Alignment of the chromosomes containing inversions (A01, A02, A06, and A13) between the 2 A1 genomes. A13 had 3 inversions. The major inversion on A13 was so large that a portion was colored as a translocation, instead of an inversion by plotsr (Goel et al. 2022).

References

    1. R Development Core Team, et al. . R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing;2011.
    1. R Core Team . R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing;2020.
    1. Adelson RP, Renton AE, Li W, Barzilai N, Atzmon G, Goate AM, Davies P, Freudenberg-Hua Y. Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance. Sci Rep. 2019;9(1):16156. doi:10.1038/s41598-019-52614-7. - DOI - PMC - PubMed
    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–410. doi:10.1016/S0022-2836(05)80360-2. - DOI - PubMed
    1. Bailly-Bechet M, Haudry A, Lerat E. “One code to find them all”: a perl tool to conveniently parse RepeatMasker output files. Mob DNA. 2014;5(1):13. doi:10.1186/1759-8753-5-13. - DOI

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