Bioinformatics-based collection and analysis of dispersed repeats

Dispersed repeats play important roles in gene expression regulation, recombination rearrangement, biogenetic diversity, disease research and therapy, and computational biology. In this study, we summarized the types and distribution of dispersed repeats in the mitochondrial genomes (mtDNA) of the genus Cotton to clarify the structure and characteristics of the mitochondrial genomes of the genus Cotton. In this study, the whole mitochondrial genomes of eight different cotton species were selected based on bioinformatics technology, and the dispersed repeats were summarized and analyzed with the combination of open-source software (REPtuer) and visualization tools. The results showed that the dispersed repeats existed in the mitochondrial genomes of eight different cotton species in common forward and palindromic repeats. The number of dispersed repeats ranged from 86 to 91 in the mitochondrial genomes of cotton, of which the number of forward repeats ranged from 47 to 90 and the number of palindromic repeats ranged from 7 to 47. In terms of length, most of the dispersed repeats were short repeats (<1000 bp), and the rest were long repeats (>1000 bp). In distribution, the dispersed repeats were widely present in intergenic sequences. Among them, short, dispersed repeats were more likely to be found in larger intergenic sequences. The dispersed repeats found in the eight cotton mtDNAs can explain the complex structure and frequent recombination and rearrangement activities of cotton mtDNAs.