Diversity Assessment of Antagonistic Trichoderma Species by Comparative Analysis of Microsatellites

Recent genome sequencing of Trichoderma species has opened the way for their diversity in the assessment and comparative analysis of microsatellites. Here, we compared microsatellites of three taxonomically different Trichoderma species such as T. asperellum, T. citrinoviride, and T. longibrachiatum. Our results highlight abundance and diversity of microsatellite patterns in all the test genomes. The highest relative abundance (283.6) with a relative density (3424.7) of SSRs was identified in all three sequence sets of T. citrinoviride. Among all three sequence sets, selection of these isolates were based on maximum frequency of SSRs which was of trinucleotide repeats (79.8%), whereas the dinucleotide repeat represented <8%. With the help of bioinformatics tools, species-specific diagnostic primers were developed and validated by silica PCR. Out of 31 primer sets, only 18 pairs of primer indicated successful amplification among all the species tested. A total of 34 alleles were detected and 7 loci have polymorphism information content (PIC) values greater than 0.40. In cross-species examination, of 31 markers, amplification of 5 of them was in the corresponding microsatellite regions of 18 different isolates of Trichoderma and showed monomorphic banding pattern. Microsatellite locus ThSSR3 was highly specific for Trichoderma, as amplification was not detected in closely related other 29 taxa. Primer set, ThSSR3F/ThSSR3R, amplified a specific amplicon of 600 bp from all Trichoderma species. According to intensive literature survey, the motif-based comparison is first reported here and was performed in recently sequenced three different species of Trichoderma.