Gossypium hirsutum (AD1) 'PSC355' genome USDA_v1

The sequencing libraries were constructed at the Brigham Young University DNA Sequencing Center (DNASC). High Molecular Weight (HMW) DNA was partitioned into 13 bins using the Sage Elf (Sage Science, Beverly, MA, USA), and the top five bins were run on a Fragment Analyzer (Agilent Technologies, Santa Clara, CA, USA) to select the appropriate bin size range (15-18 kb). Libraries were made using the SMRTbell Express Template Prep kit as recommended by Pacific Biosciences (PacBio, Menlo Park, CA, USA). Five PacBio cells were sequenced on the Pacific Biosciences Sequel II system, and the reads were assembled using hifiasm (Cheng et al. 2021) with default parameters. Manual scaffolding was used to create pseudomolecules of PSC355.  

Hi-C libraries were constructed from the same seedling tissue using the Plant Hi-C Kit (Phase Genomics, Seattle, WA, USA). Short-read sequencing (Illumina, San Diego, CA, USA; 150PE) of the libraries was performed by BGI Americas Corp (Cambridge, MA, USA). The Hi-C data was mapped to their respective assembled genome sequence using bwa mem (Li and Durbin 2009). Within their respective set of mapped reads, matlock (https://github.com/phasegenomics/matlock) was used to identify linkages between different genomic regions in the bam file. Juicebox (Durand et al. 2016) was used to visualize the linkages along the pseudomolecules.   

Centromeric locations were estimated by mapping CENH3 Chip-seq reads from leaf tissue (Hu et al. 2019). Reads from immunoprecipitated samples were compared to control samples using the deeptools program bamCompare (Ramírez et al. 2016) with visualization in IGV. Telomeric repeats and their respective lengths were manually identified in Geneious (Biomatters, Ltd.).