Pacbio reads Gtom.USDA.3
Acid-delinted seeds of G. darwinii were chipped and rolled in moist paper towels. Rolled towels were placed in an incubator set at 30C for 4 days to germinate. DNA was extracted using the Qiagen Genomic Tip kit (Qiagen, Hilden, Germany). The sequencing libraries were constructed at the Brigham Young University DNA Sequencing Center (DNASC). DNA shearing of both libraries was done on a Megaruptor2 (~20 kb) (Diagenonde Inc., Denville, NJ). HMW DNA was partitioned into 13 bin using the Sage Elf (Sage Science, Beverly, MA) and the top 5 bins were run on a Fragment Analyzer (Agilent Technologies, Santa Clara, CA) 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 (Menlo Park, CA). Five PacBio cells were sequencing from each library on the Pacific Biosciences Sequel 2 system. The PacBio reads were assembled using hifiasm (Cheng et al. 2021) using default parameters. Both assembled genomes were aligned to previously assembled genomes of G. hirsutum using minimap2 (Li 2018) and visualized by dotPlotly (https://github.com/tpoorten/dotPlotly). Manual scaffolding was used to create pseudomolecules of both genomes.