A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development Article Swipe
Sahil Mahfooz
,
Satyendra Singh
,
Ramraje Rakh
,
Arpita Bhattacharya
,
Nishtha Mishra
,
Poonam C. Singh
,
Puneet Singh Chauhan
,
Chandra Shekhar Nautiyal
,
Aradhana Mishra
·
YOU?
·
· 2016
· Open Access
·
· DOI: https://doi.org/10.3389/fmicb.2016.00575
YOU?
·
· 2016
· Open Access
·
· DOI: https://doi.org/10.3389/fmicb.2016.00575
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 Trichoderma 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.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fmicb.2016.00575
- https://www.frontiersin.org/articles/10.3389/fmicb.2016.00575/pdf
- OA Status
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- Cited By
- 25
- References
- 48
- Related Works
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- OpenAlex ID
- https://openalex.org/W2344435308
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2344435308Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3389/fmicb.2016.00575Digital Object Identifier
- Title
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A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker DevelopmentWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2016Year of publication
- Publication date
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2016-04-27Full publication date if available
- Authors
-
Sahil Mahfooz, Satyendra Singh, Ramraje Rakh, Arpita Bhattacharya, Nishtha Mishra, Poonam C. Singh, Puneet Singh Chauhan, Chandra Shekhar Nautiyal, Aradhana MishraList of authors in order
- Landing page
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https://doi.org/10.3389/fmicb.2016.00575Publisher landing page
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https://www.frontiersin.org/articles/10.3389/fmicb.2016.00575/pdfDirect link to full text PDF
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
- OA URL
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https://www.frontiersin.org/articles/10.3389/fmicb.2016.00575/pdfDirect OA link when available
- Concepts
-
Genome, Biology, Microsatellite, Genetics, Trichoderma, Gene, Botany, AlleleTop concepts (fields/topics) attached by OpenAlex
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25Total citation count in OpenAlex
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2024: 3, 2023: 2, 2022: 5, 2021: 1, 2020: 2Per-year citation counts (last 5 years)
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48Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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