Cargando…

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C. geophilum is only known from asexual states but is often considered a cryptic species complex, si...

Descripción completa

Detalles Bibliográficos
Autores principales: Vélez, Jessica M., Morris, Reese M., Vilgalys, Rytas, Labbé, Jessy, Schadt, Christopher W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787446/
https://www.ncbi.nlm.nih.gov/pubmed/33406078
http://dx.doi.org/10.1371/journal.pone.0231367
_version_ 1783632825789972480
author Vélez, Jessica M.
Morris, Reese M.
Vilgalys, Rytas
Labbé, Jessy
Schadt, Christopher W.
author_facet Vélez, Jessica M.
Morris, Reese M.
Vilgalys, Rytas
Labbé, Jessy
Schadt, Christopher W.
author_sort Vélez, Jessica M.
collection PubMed
description The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C. geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C. geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C. geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C. geophilum, we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.
format Online
Article
Text
id pubmed-7787446
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-77874462021-01-14 Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives Vélez, Jessica M. Morris, Reese M. Vilgalys, Rytas Labbé, Jessy Schadt, Christopher W. PLoS One Research Article The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C. geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C. geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C. geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C. geophilum, we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns. Public Library of Science 2021-01-06 /pmc/articles/PMC7787446/ /pubmed/33406078 http://dx.doi.org/10.1371/journal.pone.0231367 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Vélez, Jessica M.
Morris, Reese M.
Vilgalys, Rytas
Labbé, Jessy
Schadt, Christopher W.
Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives
title Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives
title_full Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives
title_fullStr Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives
title_full_unstemmed Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives
title_short Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives
title_sort phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus cenococcum geophilum associated with populus trichocarpa soils in the pacific northwest, usa and comparison to globally distributed representatives
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787446/
https://www.ncbi.nlm.nih.gov/pubmed/33406078
http://dx.doi.org/10.1371/journal.pone.0231367
work_keys_str_mv AT velezjessicam phylogeneticdiversityof200isolatesoftheectomycorrhizalfunguscenococcumgeophilumassociatedwithpopulustrichocarpasoilsinthepacificnorthwestusaandcomparisontogloballydistributedrepresentatives
AT morrisreesem phylogeneticdiversityof200isolatesoftheectomycorrhizalfunguscenococcumgeophilumassociatedwithpopulustrichocarpasoilsinthepacificnorthwestusaandcomparisontogloballydistributedrepresentatives
AT vilgalysrytas phylogeneticdiversityof200isolatesoftheectomycorrhizalfunguscenococcumgeophilumassociatedwithpopulustrichocarpasoilsinthepacificnorthwestusaandcomparisontogloballydistributedrepresentatives
AT labbejessy phylogeneticdiversityof200isolatesoftheectomycorrhizalfunguscenococcumgeophilumassociatedwithpopulustrichocarpasoilsinthepacificnorthwestusaandcomparisontogloballydistributedrepresentatives
AT schadtchristopherw phylogeneticdiversityof200isolatesoftheectomycorrhizalfunguscenococcumgeophilumassociatedwithpopulustrichocarpasoilsinthepacificnorthwestusaandcomparisontogloballydistributedrepresentatives