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A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable
Sahil Mahfooz1, Satyendra P Singh1, Ramraje Rakh2
1Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India.
Frontiers in Microbiology
|May 21, 2016
Summary
This study analyzed microsatellites in Trichoderma genomes, finding their abundance correlates with G+C content. Twelve polymorphic simple sequence repeat (SSR) markers were developed for genetic relationship studies in Trichoderma isolates.
Area of Science:
- Genomics
- Molecular Biology
- Mycology
Background:
- Members of the genus Trichoderma are globally recognized for their mycoparasitic capabilities.
- Understanding the genomic organization and evolution of Trichoderma is crucial for harnessing their potential.
Purpose of the Study:
- To investigate the occurrence, relative abundance, and density of simple sequence repeats (SSRs) in four Trichoderma species using an in silico approach.
- To develop polymorphic SSR markers for analyzing genetic relationships among Trichoderma isolates.
Main Methods:
- In silico comparative analysis of SSRs in the genomes of Trichoderma atroviride, T. harzianum, T. reesei, and T. virens.
- Evaluation of SSR motif conservation in transcript sequences.
- Development and characterization of polymorphic SSR markers.
Main Results:
- SSRs occurrence, abundance, and density varied across the four genomes and did not correlate with genome size.
- A positive correlation was observed between SSR relative abundance/density and genome G+C content.
- Tri-nucleotide repeats were the most abundant (∼38%), while hexa-nucleotide repeats were least abundant (∼10.2%).
- 49.5% conservation of SSR motifs was found in transcript sequences.
- Twelve polymorphic SSR markers were developed (6 from T. atroviride, 6 from T. harzianum).
- T. atroviride SSR markers exhibited higher polymorphism (PIC 0.745) than T. harzianum markers (PIC 0.615).
Conclusions:
- SSR distribution in Trichoderma genomes is influenced by G+C content, not genome size.
- The developed SSR markers are effective tools for assessing genetic diversity and relationships within Trichoderma populations.
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