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Title: 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 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. We used methods developed to interrogate both assembled and unassembled sequences, and 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 providemore » 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.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [4] ;  [4] ;  [1]
  1. Harvard Univ., Cambridge, MA (United States). Department of Organismic and Evolutionary Biology
  2. Harvard Univ., Cambridge, MA (United States). Department of Organismic and Evolutionary Biology; Univ. of Oslo (Norway)
  3. Harvard Univ., Cambridge, MA (United States). Department of Organismic and Evolutionary Biology; Harvard Univ., Cambridge, MA (United States). FAS Center for Systems Biology
  4. U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA (United States)
Publication Date:
Report Number(s):
LBNL-178150
Journal ID: ISSN 1759-6653; ir:178150
Grant/Contract Number:
AC02-05CH11231; 1021606; NFR 209194
Type:
Accepted Manuscript
Journal Name:
Genome Biology and Evolution
Additional Journal Information:
Journal Volume: 6; Journal Issue: 7; Journal ID: ISSN 1759-6653
Publisher:
Society for Molecular Biology and Evolution
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; evolution of symbiosis; genome architecture; phylogeny; repetitive DNA; ecological genomics
OSTI Identifier:
1247474

Hess, Jaqueline, Skrede, Inger, Wolfe, Benjamin E., LaButti, Kurt, Ohm, Robin A., Grigoriev, Igor V., and Pringle, Anne. Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi. United States: N. p., Web. doi:10.1093/gbe/evu121.
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. United States. doi:10.1093/gbe/evu121.
Hess, Jaqueline, Skrede, Inger, Wolfe, Benjamin E., LaButti, Kurt, Ohm, Robin A., Grigoriev, Igor V., and Pringle, Anne. 2014. "Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi". United States. doi:10.1093/gbe/evu121. https://www.osti.gov/servlets/purl/1247474.
@article{osti_1247474,
title = {Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi},
author = {Hess, Jaqueline and Skrede, Inger and Wolfe, Benjamin E. and LaButti, Kurt and Ohm, Robin A. and Grigoriev, Igor V. and Pringle, Anne},
abstractNote = {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. We used methods developed to interrogate both assembled and unassembled sequences, and 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.},
doi = {10.1093/gbe/evu121},
journal = {Genome Biology and Evolution},
number = 7,
volume = 6,
place = {United States},
year = {2014},
month = {6}
}