Short Tandem Repeats in plants: genomic distribution and function prediction

Abstract Background Short Tandem repeats (STR) existed as popular elements in both eukaryotic and prokaryotic genomes. Results In this study, we analyzed the characteristics, distributions, motif features of STRs within whole-genomes of 140 plant species. The results showed that STRs density was negatively correlated with the genome size. Hexa-nucleotide repeat was the most abundant type of STRs. The distribution of algae shows a preference different from that of other plants. By analyzing GC-contents of STRs and genome, it was concluded that STRs motif was influenced by GC-contents. Analysis of the long STRs in genome (length ≥ 1000bp) found that dicots have the more long STRs. For STRs types, di- and tri-nucleotide accounted for the highest proportion. Analyzing and designing long STRs in CDS (length ≥ 500bp) was to verify the role of long STRs in Gossypium hirsutumTM-1 and Solanum tuberosum. By comparing the long STRs found in Fragaria x ananassa with other species, some evolutionary characteristics of the long STRs were obtained. Conclusions We got the characteristics, distribution and motif features of STRs in the whole genome of 140 plants, and obtained some evolutionary characteristics of long STRs. The study provides useful insights into STRs preference, characteristics and distribution in plants.