AUTHOR=Mahfooz Sahil , Singh Satyendra P. , Rakh Ramraje , Bhattacharya Arpita , Mishra Nishtha , Singh Poonam C. , Chauhan Puneet S. , Nautiyal Chandra S. , Mishra Aradhana 

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

JOURNAL=Frontiers in Microbiology

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2016.00575

DOI=10.3389/fmicb.2016.00575

ISSN=1664-302X

ABSTRACT=<p>Members of genus <italic>Trichoderma</italic> are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an <italic>in silico</italic> approach to compare the occurrence, relative abundance and density of SSRs in <italic>Trichoderma atroviride</italic>, <italic>T. harzianum</italic>, <italic>T. reesei</italic>, and <italic>T. virens</italic>. 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 <italic>T. reesei</italic> whereas it was least in second smallest genome of <italic>T. atroviride.</italic> 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 <italic>Trichoderma</italic> isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from <italic>T. atroviride</italic> and remaining 6 belong to <italic>T. harzianum</italic>. SSR markers were found to be more polymorphic from <italic>T. atroviride</italic> with an average polymorphism information content value of 0.745 in comparison with <italic>T. harzianum</italic> (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 <italic>Trichoderma</italic>.</p>