Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity
Molecular markers that enable monitoring of fungi in their natural environment or assist in the identification of specific strains would facilitate Trichoderma utilization, particularly as an agricultural biocontrol agent (BCA). In this study, sequence analysis of internal transcribed spacer regions...
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| Format: | Online |
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Springer Netherlands
2015
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445485/ |
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pubmed-44454852015-06-01 Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity Skoneczny, Dominik Oskiera, Michał Szczech, Magdalena Bartoszewski, Grzegorz Article Molecular markers that enable monitoring of fungi in their natural environment or assist in the identification of specific strains would facilitate Trichoderma utilization, particularly as an agricultural biocontrol agent (BCA). In this study, sequence analysis of internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) of the ribosomal RNA (rRNA) gene cluster, a fragment of the translation elongation factor 1-alpha (tef1) gene, and random amplified polymorphic DNA (RAPD) markers were applied to determine the genetic diversity of Trichoderma atroviride strains collected in Poland, and also in order to identify loci and PCR-based molecular markers useful in genetic variation assessment of that fungus. Although tef1 and RAPD analysis showed limited genetic diversity among T. atroviride strains collected in Poland, it was possible to distinguish major groups that clustered most of the analyzed strains. Polymorphic RAPD amplicons were cloned and sequenced, yielding sequences representing 13 T. atroviride loci. Based on these sequences, a set of PCR-based markers specific to T. atroviride was developed and examined. Three cleaved amplified polymorphic sequence (CAPS) markers could assist in distinguishing T. atroviride strains. The genomic regions identified may be useful for further exploration and development of more precise markers suitable for T. atroviride identification and monitoring, especially in environmental samples. Springer Netherlands 2015-03-20 2015 /pmc/articles/PMC4445485/ /pubmed/25791292 http://dx.doi.org/10.1007/s12223-015-0385-z Text en © The Author(s) 2015 Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Skoneczny, Dominik Oskiera, Michał Szczech, Magdalena Bartoszewski, Grzegorz |
| spellingShingle |
Skoneczny, Dominik Oskiera, Michał Szczech, Magdalena Bartoszewski, Grzegorz Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity |
| author_facet |
Skoneczny, Dominik Oskiera, Michał Szczech, Magdalena Bartoszewski, Grzegorz |
| author_sort |
Skoneczny, Dominik |
| title |
Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity |
| title_short |
Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity |
| title_full |
Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity |
| title_fullStr |
Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity |
| title_full_unstemmed |
Genetic diversity of Trichoderma atroviride strains collected in Poland and identification of loci useful in detection of within-species diversity |
| title_sort |
genetic diversity of trichoderma atroviride strains collected in poland and identification of loci useful in detection of within-species diversity |
| description |
Molecular markers that enable monitoring of fungi in their natural environment or assist in the identification of specific strains would facilitate Trichoderma utilization, particularly as an agricultural biocontrol agent (BCA). In this study, sequence analysis of internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) of the ribosomal RNA (rRNA) gene cluster, a fragment of the translation elongation factor 1-alpha (tef1) gene, and random amplified polymorphic DNA (RAPD) markers were applied to determine the genetic diversity of Trichoderma atroviride strains collected in Poland, and also in order to identify loci and PCR-based molecular markers useful in genetic variation assessment of that fungus. Although tef1 and RAPD analysis showed limited genetic diversity among T. atroviride strains collected in Poland, it was possible to distinguish major groups that clustered most of the analyzed strains. Polymorphic RAPD amplicons were cloned and sequenced, yielding sequences representing 13 T. atroviride loci. Based on these sequences, a set of PCR-based markers specific to T. atroviride was developed and examined. Three cleaved amplified polymorphic sequence (CAPS) markers could assist in distinguishing T. atroviride strains. The genomic regions identified may be useful for further exploration and development of more precise markers suitable for T. atroviride identification and monitoring, especially in environmental samples. |
| publisher |
Springer Netherlands |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445485/ |
| _version_ |
1613228202448125952 |