Figure: DePaul University Assistant Professor Thiru Ramaraj and alumna Azalea Mendoza have published one of the most complete genomes of a top species of cotton. Photo Source: DePaul University/Jeff Carrion

Computer scientists at DePaul University in the United States used a bioinformatics workflow to reconstruct one of the most complete genomes of a top cotton species, the African domesticated Gossypium herbaceum cultivar Wagad, giving scientists a more complete picture of how wild cotton was domesticated over time.

The research team is led by Thiru Ramaraj, assistant professor of computer science at DePaul's Jarvis College of Computing and Digital Media and also the lead author of the publication in the journal G3: Genes, Genomes, Genetics. Their work began with crunching DNA sequence data. They reconstructed the Wagad genome by assembling high-quality long DNA sequence data generated using Pacific Biosciences sequencing technology. They then used whole genome maps from Bionano genomics to order and orient the initial assembly. Lastly, they used Hi-C sequence data from Phase genomics to construct chromosome level genome.

Computer science graduate student Azalea Mendoza helped the team and conducted research on the history of cotton to zoom out and understand “the big picture.” She found that everywhere cotton is grown, it is primarily used for fiber. Using comparative genomics, Mendoza looked for variations against its closest relative and to an outgroup. She also looked into annotated genes and noted their functions, finding that many genes were related to the content of fiber.

For more details, read the news article in DePaul Newsroom or the open-access paper in G3: Genes, Genomes, Genetics.

https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=20277