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Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains

Biological control agents (BCA) are beneficial organisms that are applied to protect plants from pests. Many fungi of the genus Trichoderma are successful BCAs but the underlying mechanisms are not yet fully understood. Trichoderma cf. atroviride strain LU132 is a remarkably effective BCA compared t...

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Autores principales: Lange, Claudia, Weld, Richard J., Cox, Murray P., Bradshaw, Rosie E., McLean, Kirstin L., Stewart, Alison, Steyaert, Johanna M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868595/
https://www.ncbi.nlm.nih.gov/pubmed/27190719
http://dx.doi.org/10.7717/peerj.2023
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author Lange, Claudia
Weld, Richard J.
Cox, Murray P.
Bradshaw, Rosie E.
McLean, Kirstin L.
Stewart, Alison
Steyaert, Johanna M.
author_facet Lange, Claudia
Weld, Richard J.
Cox, Murray P.
Bradshaw, Rosie E.
McLean, Kirstin L.
Stewart, Alison
Steyaert, Johanna M.
author_sort Lange, Claudia
collection PubMed
description Biological control agents (BCA) are beneficial organisms that are applied to protect plants from pests. Many fungi of the genus Trichoderma are successful BCAs but the underlying mechanisms are not yet fully understood. Trichoderma cf. atroviride strain LU132 is a remarkably effective BCA compared to T. cf. atroviride strain LU140 but these strains were found to be highly similar at the DNA sequence level. This unusual combination of phenotypic variability and high DNA sequence similarity between separately isolated strains prompted us to undertake a genome comparison study in order to identify DNA polymorphisms. We further investigated if the polymorphisms had functional effects on the phenotypes. The two strains were clearly identified as individuals, exhibiting different growth rates, conidiation and metabolism. Superior pathogen control demonstrated by LU132 depended on its faster growth, which is a prerequisite for successful distribution and competition. Genome sequencing identified only one non-synonymous single nucleotide polymorphism (SNP) between the strains. Based on this SNP, we successfully designed and validated an RFLP protocol that can be used to differentiate LU132 from LU140 and other Trichoderma strains. This SNP changed the amino acid sequence of SERF, encoded by the previously undescribed single copy gene “small EDRK-rich factor” (serf). A deletion of serf in the two strains did not lead to identical phenotypes, suggesting that, in addition to the single functional SNP between the nearly clonal Trichoderma cf. atroviride strains, other non-genomic factors contribute to their phenotypic variation. This finding is significant as it shows that genomics is an extremely useful but not exhaustive tool for the study of biocontrol complexity and for strain typing.
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spelling pubmed-48685952016-05-17 Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains Lange, Claudia Weld, Richard J. Cox, Murray P. Bradshaw, Rosie E. McLean, Kirstin L. Stewart, Alison Steyaert, Johanna M. PeerJ Genetics Biological control agents (BCA) are beneficial organisms that are applied to protect plants from pests. Many fungi of the genus Trichoderma are successful BCAs but the underlying mechanisms are not yet fully understood. Trichoderma cf. atroviride strain LU132 is a remarkably effective BCA compared to T. cf. atroviride strain LU140 but these strains were found to be highly similar at the DNA sequence level. This unusual combination of phenotypic variability and high DNA sequence similarity between separately isolated strains prompted us to undertake a genome comparison study in order to identify DNA polymorphisms. We further investigated if the polymorphisms had functional effects on the phenotypes. The two strains were clearly identified as individuals, exhibiting different growth rates, conidiation and metabolism. Superior pathogen control demonstrated by LU132 depended on its faster growth, which is a prerequisite for successful distribution and competition. Genome sequencing identified only one non-synonymous single nucleotide polymorphism (SNP) between the strains. Based on this SNP, we successfully designed and validated an RFLP protocol that can be used to differentiate LU132 from LU140 and other Trichoderma strains. This SNP changed the amino acid sequence of SERF, encoded by the previously undescribed single copy gene “small EDRK-rich factor” (serf). A deletion of serf in the two strains did not lead to identical phenotypes, suggesting that, in addition to the single functional SNP between the nearly clonal Trichoderma cf. atroviride strains, other non-genomic factors contribute to their phenotypic variation. This finding is significant as it shows that genomics is an extremely useful but not exhaustive tool for the study of biocontrol complexity and for strain typing. PeerJ Inc. 2016-05-12 /pmc/articles/PMC4868595/ /pubmed/27190719 http://dx.doi.org/10.7717/peerj.2023 Text en ©2016 Lange et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Genetics
Lange, Claudia
Weld, Richard J.
Cox, Murray P.
Bradshaw, Rosie E.
McLean, Kirstin L.
Stewart, Alison
Steyaert, Johanna M.
Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains
title Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains
title_full Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains
title_fullStr Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains
title_full_unstemmed Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains
title_short Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains
title_sort genome-scale investigation of phenotypically distinct but nearly clonal trichoderma strains
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868595/
https://www.ncbi.nlm.nih.gov/pubmed/27190719
http://dx.doi.org/10.7717/peerj.2023
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