Gossypium herbaceum (A1) 'Wagad' genome USDA_v1

About the assembly

Here we report a genome assembly of Gossypium herbaceum (variety 'Wagad', A1-0135, PI 630010) that complements the existing genome assemblies and diversity studies (Huang et al. 2020). Our data provide a foundation for understanding the transition from wild to domesticated G. herbaceum, thereby providing an additional perspective on the commonalities of domestication in multiple cotton species.

PacBio CCS reads were assembled using Hifiasm, a fast haplotype-resolved de novo genome assembler for PacBio HiFi sequence reads (Cheng et al. 2021). The contigs were aligned to previously assembled genomes of G. herbaceum and G. arboreum (Huang et al. 2020) using minimap2 (Li 2018) and visualized by dotPlotly (https://github.com/tpoorten/dotPlotly). Multiple contigs aligning to the same contig were manually scaffolded (or concatenated) to create the final chromosomes. The final chromosomes were labeled and again aligned to the previously published A-genome using minimap2 and visualized by dotPlotly.

Hi-C libraries were constructed by Phase Genomics (Seattle, WA) from seedling tissue grown at Brigham Young University Greenhouses (different tissue source than sequenced by PacBio above). Short-read sequencing (Illumina, San Diego, CA; 150PE) of the libraries was performed by PhaseGenomics. The Hi-C data was mapped to the assembled genome sequence using bwa mem (with the -5SP option for HiC data, Li and Durbin 2009). The Hi-C interactions were used as evidence for contig proximity and in scaffolding contig sequences. Matlock (https://github.com/phasegenomics/matlock) was used in conjunction with the mapped reads to identify linkages between different genomic regions in the bam file. Juicebox (Robinson et al. 2018) was used to visualize the linkages along the pseudomolecules. All inversions were identified in alignments created by minimap2 (Li 2018).

Publication: Ramaraj T, et al. (2022) The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication. bioRxiv. https://doi.org/10.1101/2022.06.07.494775