Genome-wide microsatellites and species specific markers in genus revealed through whole genome analysis.

Genome wide microsatellite maps shall support systematics through the development of reliable markers, enabling species discrimination and variability analyses. Whole genome sequences of 17 accessions belonging to 14 species were retrieved from GenBank and the genome-wide microsatellites in each species were mined. A total of 51,200 microsatellites, including dinucleotide to decanucleotide motifs, have been identified across all the species and each one was characterized for uniqueness and repeat number. The T30-4 genome had the highest (6873) and 3378 had the lowest number of microsatellites (1802). Dinucleotide motifs (63.6%) followed by trinucleotide motifs (30.1%) were most abundant in all the genome. From 14 species, 250 microsatellites which are unique for the respective genomes are detailed along with their primer combinations and product sizes. had the highest number of unique microsatellite motifs. Genome wide microsatellite maps for all the 14 species including the chromosome, position, motif, repeat number, forward and reverse primer sequences and expected PCR product size, for every microsatellite are presented. Markers based on the unique microsatellites could be used to identify each species, whereas the ones common to all species could be used to identify the genetic variability. Furthermore, to confirm the results, pure cultures of , and were procured from the Repository, DNA was isolated and the unique markers were screened across the species. The characteristic markers developed have confirmed the genome analysis results.