Repeats were identified using a combination of RepeatMasker and "One code to find them all", the latter of which assembles multiple adjacent RepeatMasker hits into complete transposable element (TE) copies. RepeatMasker was run fore each genome with a custom library, which combines Repbase 23.04 repeats with cotton-specific repeats. Parameters are available at https://github.com/Wendellab/D5D10. "One code to find them all" was used to aggregate multiple hits into TE models using default parameters. All code can be found at https://github.com/Wendellab/D5D10

Multi-string Burows-Wheeler transform (BWT) description for each whole genome dataset (optional; instructions at https://github.com/holtjma/msbwt/wiki/Converting-to-msbwt's-RLE-format)

Data availability listing where to access all raw reads, processed data, BWTs, and other relevant data