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.