Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant...

Full description

Bibliographic Details
Main Authors:	Hess, Jaqueline, Skrede, Inger, Wolfe, Benjamin E., LaButti, Kurt, Ohm, Robin A., Grigoriev, Igor V., Pringle, Anne
Format:	Online
Language:	English
Published:	Oxford University Press 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122921/

id	pubmed-4122921
recordtype	oai_dc
spelling	pubmed-41229212014-08-12 Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi Hess, Jaqueline Skrede, Inger Wolfe, Benjamin E. LaButti, Kurt Ohm, Robin A. Grigoriev, Igor V. Pringle, Anne Research Article Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture. Oxford University Press 2014-06-12 /pmc/articles/PMC4122921/ /pubmed/24923322 http://dx.doi.org/10.1093/gbe/evu121 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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	Hess, Jaqueline Skrede, Inger Wolfe, Benjamin E. LaButti, Kurt Ohm, Robin A. Grigoriev, Igor V. Pringle, Anne
spellingShingle	Hess, Jaqueline Skrede, Inger Wolfe, Benjamin E. LaButti, Kurt Ohm, Robin A. Grigoriev, Igor V. Pringle, Anne Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
author_facet	Hess, Jaqueline Skrede, Inger Wolfe, Benjamin E. LaButti, Kurt Ohm, Robin A. Grigoriev, Igor V. Pringle, Anne
author_sort	Hess, Jaqueline
title	Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
title_short	Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
title_full	Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
title_fullStr	Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
title_full_unstemmed	Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
title_sort	transposable element dynamics among asymbiotic and ectomycorrhizal amanita fungi
description	Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture.
publisher	Oxford University Press
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122921/
_version_	1613121275019919360

Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi

Similar Items