A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development

Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in-silico approach to compare the occurrence, relative abundance and density of SSRs in T.atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G+C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ~38%, whereas hexa-nuceotide repeats were the least (~10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma

A Comparison of Microsatellites in Phytopathogenic Aspergillus Species in Order to Develop Markers for the Assessment of Genetic Diversity among Its Isolates

The occurrence of Microsatellites (SSRs) has been witnessed in most of the fungal genomes however its abundance varies across species. In the present study, we analyzed the frequency of SSRs in the whole genome and transcripts of two phyto-pathogenic (Aspergillus niger and Aspergillus terreus) and compared them with two non-pathogenic (Aspergillus nidulans and Aspergillus oryzae) Aspergillus. Higher relative abundance and relative density of SSRs were observed in the whole genome and transcript sequences of the pathogenic Aspergillus when compared to the non-pathogenic. The relative abundance and density of SSRs were positively correlated with the G+C content of transcripts. Among the different classes of SSR, the percentage of tetra-nucleotide SSRs were maximum in A. niger (36.7%) and A. oryzae (35.9%) whereas A. nidulans and A. terreus preferred tri-nucleotide SSRs (38.2 and 42.1%) in whole genome sequences. In transcripts, tri-nucleotide SSRs were the most abundant whereas di-nucleotide SSRs were the least favored. Motif conservation study among the transcripts revealed conservation of only 27% motif within Aspergillus species. Furthermore, a similar relationship among the Ascomycetes was obtained on the basis of motif conservation and conserved genes (rDNA). To analyze the diversity present within the Indian isolates of Aspergillus, primers were successfully designed for 692 motifs in A. niger and A. terreus of which 20 were selected for diversity analysis. Among all the markers amplified, 10 markers (83.3%) were polymorphic, whereas remaining two markers (16.6%) were monomorphic. Ten polymorphic markers acquired in this investigation showed the utility of recently created SSR markers in the assessment of genetic diversity among various isolates of Aspergillus

Conservation of microsatellite regions across legume genera increases marker repertoire in pigeonpea

Abstract Microsatellite markers from chickpea, common bean, fieldpea and lentil were studied for their transferability and ability to reveal polymorphism in pigeonpea with an objective to use them in linkage map construction and tagging of agronomically important traits. Out of total one hundred and sixty three genic and genomic markers from four legume genera screened on six pigeonpea genotypes, 58 were found to be transferable in pigeonpea. Maximum transferability (47%) was shown by markers from common bean, followed by lentil, fieldpea and chickpea. The average polymorphism information content value with genic and genomic markers was found to be 0.60 to 0.50 respectively. These transferable markers will add to the pool of available markers for genotyping and mapping of important traits in Cajanus. This study also demonstrated that genic markers are not only transferable across genera but also are at par with genomic markers in detecting polymorphism

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Not AvailableTo study the conservation of microsatellite regions, a set of 137 microsatellite markers developed from Phaseolus, Cajanus, Lens and Cicer genera of Leguminosae family were tested for their transferability across 16 genotypes of Phaseolus belonging to diverse collections from South America and Asia. Considerable transferability was observed with markers derived from Cajanus (60%), Lens (46%) and Cicer (28%). Of the total 122 loci were amplified, 82 cross-species polymorphic amplicons were obtained. Maximum number of alleles per marker was six (Cicer markers). Polymorphism information content values ranged from 0.12 to 0.96 with Cajanus, 0.13 to 0.74 with Lens and 0.30 to 0.93 with Cicer markers. Unweighted pair group method employing arithmetic averages cluster analysis of Phaseolus genotypes showed clear demarcation between the commercial cultivars falling in separate cluster with respect to their seed size and maturity. Transferability of genomic SSRs was different from that of expressed sequence tag-derived genic microsatellite markers.Not Availabl

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