Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data
Artikel i vetenskaplig tidskrift, 2011

An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.

multiple alignment

fungi

ITS

Environmental sampling

phylogenetic analysis

Författare

R. Henrik Nilsson

Göteborgs universitet

Francesc Lopez-Giraldez

Wen-ying Zhuang

Yu-cheng Dai

Peter R. Johnston

Jeffrey P. Townsend

PLoS ONE

1932-6203 (ISSN)

Vol. 6 4 e19039-

Ämneskategorier

Biologisk systematik

Markvetenskap

Ekologi

Mikrobiologi

Bioinformatik och systembiologi

DOI

10.1371/journal.pone.0019039

PubMed

21533038