Prediction of microsatellites and the annotation of repeat sequences in partial coconut genome

Microsatellites or simple sequence repeats (SSRs) are sequences in which one or a few bases are tandemly repeated ranging from 1–6 base pair long units. They are functioned as important molecular markers for genetic diversity, linkage mappingandmolecular breeding. Coconut, datepalm, andoil palmarecultivated commercially in India andthe bioinformatics predictions of microsatellites in these palms are of having importance in crop improvement. A total of 22,76,863 filtered reads of 917 Mb of partial coconut genomic sequences were generated through 454 sequencing. We have adopted Anvaya pipeline for sequence processing in which Seqclean and CAP3 tools were connected for the preliminary sequence cleaning for sequence contamination and assembly of coconut partial genome sequences. These sequences were used as input for the succeeding SSR mining processes. SSRs were located in the sequences by using microsatellite identification tool, MISA. In coconut, a total of 27,964 SSRs were detected in 24,960 sequences after screening the mono repeats. The microsatellites were occurred with an average of one SSR/17.4 Kb in coconut. Di-nucleotide repeats were found to be abundant in coconut (69.02%) followed by tri-(22.89%) and tetra-(5.48%) repeats, respectively. Among the di-type repeats AT/TA/AG/GA repeats contributed around 42% of the total SSRs. Thus coconut genome is found to be the richest source of microsatellite repeats and the complete detection of SSRs remained incomplete for the unexplored genome regions of this palm.