Genome-wide investigation and analysis of microsatellites and compound microsatellites in Leptolyngbya species, Cyanobacteria

Abstract Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in 36 genomes of Leptolyngbya. The results disclosed diversified patterns of distribution, abundance, density and diversity of SSRs and CSSRs in Leptolyngbya genomes. The numbers of SSRs and CSSRs were extremely uneven distributed among genomes, ranging from 11,086 to 27,292 and from 286 to 1,102, respectively. Mononucleotide SSRs were the most abundant category in 14 genomes, while the other 22 genomes followed the pattern: di- > mono- > trinucleotide SSRs. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly correlated with genome size (P  0.05). Moreover, the motif (A/T)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 33 genomes. This study provides the first insight into SSRs and CSSRs in Leptolyngbya genomes and will be useful to contribute to future use as molecular markers in closely-related species.