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Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass

BACKGROUND: Perennial ryegrass (Lolium perenne L.) is one of the most important species for temperate pastoral agriculture, forming associations with genetically diverse groups of mutualistic fungal endophytes. However, only two taxonomic groups (E. festucae var. lolii and LpTG-2) have so far been d...

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Autores principales: Hettiarachchige, Inoka K, Ekanayake, Piyumi N, Mann, Ross C, Guthridge, Kathryn M, Sawbridge, Timothy I, Spangenberg, German C, Forster, John W
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458015/
https://www.ncbi.nlm.nih.gov/pubmed/25902799
http://dx.doi.org/10.1186/s12862-015-0349-6
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author Hettiarachchige, Inoka K
Ekanayake, Piyumi N
Mann, Ross C
Guthridge, Kathryn M
Sawbridge, Timothy I
Spangenberg, German C
Forster, John W
author_facet Hettiarachchige, Inoka K
Ekanayake, Piyumi N
Mann, Ross C
Guthridge, Kathryn M
Sawbridge, Timothy I
Spangenberg, German C
Forster, John W
author_sort Hettiarachchige, Inoka K
collection PubMed
description BACKGROUND: Perennial ryegrass (Lolium perenne L.) is one of the most important species for temperate pastoral agriculture, forming associations with genetically diverse groups of mutualistic fungal endophytes. However, only two taxonomic groups (E. festucae var. lolii and LpTG-2) have so far been described. In addition to these two well-characterised taxa, a third distinct group of previously unclassified perennial ryegrass-associated endophytes was identified as belonging to a putative novel taxon (or taxa) (PNT) in a previous analysis based on simple sequence repeat (SSR) marker diversity. As well as genotypic differences, distinctive alkaloid production profiles were observed for members of the PNT group. RESULTS: A detailed phylogenetic analysis of perennial ryegrass-associated endophytes using components of whole genome sequence data was performed using complete sequences of 7 nuclear protein-encoding genes. Three independently selected genes (encoding a DEAD/DEAH box helicase [Sbp4], a glycosyl hydrolase [family 92 protein] and a MEAB protein), none of which have been previously used for taxonomic studies of endophytes, were selected together with the frequently used ‘house-keeping’ genes tefA and tubB (encoding translation elongation factor 1-α and β-tubulin, respectively). In addition, an endophyte-specific gene (perA for peramine biosynthesis) and the fungal-specific MT genes for mating-type control were included. The results supported previous phylogenomic inferences for the known species, but revealed distinctive patterns of diversity for the previously unclassified endophyte strains, which were further proposed to belong to not one but two distinct novel taxa. Potential progenitor genomes for the asexual endophytes among contemporary teleomorphic (sexual Epichloë) species were also identified from the phylogenetic analysis. CONCLUSIONS: Unique taxonomic status for the PNT was confirmed through comparison of multiple nuclear gene sequences, and also supported by evidence from chemotypic diversity. Analysis of MT gene idiomorphs further supported a predicted independent origin of two distinct perennial ryegrass-associated novel taxa, designated LpTG-3 and LpTG-4, from different members of a similar founder population related to contemporary E. festucae. The analysis also provided higher resolution to the known progenitor contributions of previously characterised perennial ryegrass-associated endophyte taxa. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-015-0349-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-44580152015-06-07 Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass Hettiarachchige, Inoka K Ekanayake, Piyumi N Mann, Ross C Guthridge, Kathryn M Sawbridge, Timothy I Spangenberg, German C Forster, John W BMC Evol Biol Research Article BACKGROUND: Perennial ryegrass (Lolium perenne L.) is one of the most important species for temperate pastoral agriculture, forming associations with genetically diverse groups of mutualistic fungal endophytes. However, only two taxonomic groups (E. festucae var. lolii and LpTG-2) have so far been described. In addition to these two well-characterised taxa, a third distinct group of previously unclassified perennial ryegrass-associated endophytes was identified as belonging to a putative novel taxon (or taxa) (PNT) in a previous analysis based on simple sequence repeat (SSR) marker diversity. As well as genotypic differences, distinctive alkaloid production profiles were observed for members of the PNT group. RESULTS: A detailed phylogenetic analysis of perennial ryegrass-associated endophytes using components of whole genome sequence data was performed using complete sequences of 7 nuclear protein-encoding genes. Three independently selected genes (encoding a DEAD/DEAH box helicase [Sbp4], a glycosyl hydrolase [family 92 protein] and a MEAB protein), none of which have been previously used for taxonomic studies of endophytes, were selected together with the frequently used ‘house-keeping’ genes tefA and tubB (encoding translation elongation factor 1-α and β-tubulin, respectively). In addition, an endophyte-specific gene (perA for peramine biosynthesis) and the fungal-specific MT genes for mating-type control were included. The results supported previous phylogenomic inferences for the known species, but revealed distinctive patterns of diversity for the previously unclassified endophyte strains, which were further proposed to belong to not one but two distinct novel taxa. Potential progenitor genomes for the asexual endophytes among contemporary teleomorphic (sexual Epichloë) species were also identified from the phylogenetic analysis. CONCLUSIONS: Unique taxonomic status for the PNT was confirmed through comparison of multiple nuclear gene sequences, and also supported by evidence from chemotypic diversity. Analysis of MT gene idiomorphs further supported a predicted independent origin of two distinct perennial ryegrass-associated novel taxa, designated LpTG-3 and LpTG-4, from different members of a similar founder population related to contemporary E. festucae. The analysis also provided higher resolution to the known progenitor contributions of previously characterised perennial ryegrass-associated endophyte taxa. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-015-0349-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-04-24 /pmc/articles/PMC4458015/ /pubmed/25902799 http://dx.doi.org/10.1186/s12862-015-0349-6 Text en © Hettiarachchige et al. 2015 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, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Hettiarachchige, Inoka K
Ekanayake, Piyumi N
Mann, Ross C
Guthridge, Kathryn M
Sawbridge, Timothy I
Spangenberg, German C
Forster, John W
Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass
title Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass
title_full Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass
title_fullStr Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass
title_full_unstemmed Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass
title_short Phylogenomics of asexual Epichloë fungal endophytes forming associations with perennial ryegrass
title_sort phylogenomics of asexual epichloë fungal endophytes forming associations with perennial ryegrass
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458015/
https://www.ncbi.nlm.nih.gov/pubmed/25902799
http://dx.doi.org/10.1186/s12862-015-0349-6
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