Table S1. Repeat sequences of 476 types of motifs Table S2. Frequency of different motifs in sub genome At, Dt and whole genome of G. barbadense cv. Xinhai21 Table S3. Information of SSR marker primer sets Table S4. Information of monomorphic SSR marker primer sets Table S5. GO and KEGG enrichment for genes of G. barbadense cv. Xinhai21 Table S6. GO and KEGG enrichment for genes containing SSR markers Table S7. Sequences of 300 SSR primer pairs selected to experimental validate the polymorphism of SSR Table S8. Detail information of 30 G. hirsutum and 27 G. barbadense accessions Table S9 Number and average density of SSR markers developed in different plant species