Thiruvarangan Ramaraj, Corrinne E Grover, Azalea C Mendoza, Mark A Arick, II, Josef J Jareczek, Alexis G Leach, Daniel G Peterson, Jonathan F Wendel, Joshua A Udall

G3 Genes|Genomes|Genetics, Volume 13, Issue 2, February 2023, jkac308, 

https://doi.org/10.1093/g3journal/jkac308

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.

See https://academic.oup.com/g3journal/article/13/2/jkac308/6858943?login=false

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