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Genome Biol Evol. 2014 Jun 12;6(7):1564-78. doi: 10.1093/gbe/evu121.

Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.

Author information

1
Department of Organismic and Evolutionary Biology, Harvard University jaqueline.hess@ibv.uio.no.
2
Department of Organismic and Evolutionary Biology, Harvard UniversitySection for Genetics and Evolutionary Biology, University of Oslo, Norway.
3
Department of Organismic and Evolutionary Biology, Harvard UniversityFAS Center for Systems Biology, Harvard University.
4
U.S. Department of Energy Joint Genome Institute, Walnut Creek, California.
5
Department of Organismic and Evolutionary Biology, Harvard University.

Abstract

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.

KEYWORDS:

ecological genomics; evolution of symbiosis; genome architecture; phylogeny; repetitive DNA

PMID:
24923322
PMCID:
PMC4122921
DOI:
10.1093/gbe/evu121
[Indexed for MEDLINE]
Free PMC Article

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