In silico comparative analysis of EST-SSRs in three cotton genomes

Abstract

In this study, expressed sequence tags- simple sequence repeat (EST-SSRs) were surveyed in three cotton genomes (Gossypium arboreum, Ga; Gossypium raimondii, Gr and Gossypium hirsutum, Gh). The frequency of EST-SSRs was highest in Gr, and motif type for hexanucleotide was obviously abundant in Gr. Trinucleotide repeats were the most abundant motif; AT and AG, AAG and ATC were the most frequent motifs for dinucleotide and trinucleotide, respectively. The repeat number was greatly diverse between the three genomes with the highest variation in Gh. AG and AAG had a high frequency both in homologue groups (HGs) with and without repeat number change between genomes. The range of repeat number change in each HG was wider in Gr-Gh. The annotation of the SSR-ESTs showed that more Gene Ontology (GO) items targeted by SSR-ESTs of Ga and Gr than those of Gh. This study gave us new insights into the difference between the three cotton genomes, which will be more helpful to understand the differentiation and evolution of the three genomes.

Key words: Cotton, simple sequence repeat, expressed sequence tags, motif, gene ontology.