Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.

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,...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Zheng Wang, R Henrik Nilsson, Francesc Lopez-Giraldez, Wen-ying Zhuang, Yu-cheng Dai, Peter R Johnston, Jeffrey P Townsend
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d63b036715764f18b3730924bbab8e14
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:d63b036715764f18b3730924bbab8e14
record_format	dspace
spelling	oai:doaj.org-article:d63b036715764f18b3730924bbab8e142021-11-18T06:55:23ZTasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.1932-620310.1371/journal.pone.0019039https://doaj.org/article/d63b036715764f18b3730924bbab8e142011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21533038/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203An 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.Zheng WangR Henrik NilssonFrancesc Lopez-GiraldezWen-ying ZhuangYu-cheng DaiPeter R JohnstonJeffrey P TownsendPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e19039 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zheng Wang R Henrik Nilsson Francesc Lopez-Giraldez Wen-ying Zhuang Yu-cheng Dai Peter R Johnston Jeffrey P Townsend Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.
description	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.
format	article
author	Zheng Wang R Henrik Nilsson Francesc Lopez-Giraldez Wen-ying Zhuang Yu-cheng Dai Peter R Johnston Jeffrey P Townsend
author_facet	Zheng Wang R Henrik Nilsson Francesc Lopez-Giraldez Wen-ying Zhuang Yu-cheng Dai Peter R Johnston Jeffrey P Townsend
author_sort	Zheng Wang
title	Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.
title_short	Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.
title_full	Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.
title_fullStr	Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.
title_full_unstemmed	Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.
title_sort	tasting soil fungal diversity with earth tongues: phylogenetic test of saté alignments for environmental its data.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/d63b036715764f18b3730924bbab8e14
work_keys_str_mv	AT zhengwang tastingsoilfungaldiversitywithearthtonguesphylogenetictestofsatealignmentsforenvironmentalitsdata AT rhenriknilsson tastingsoilfungaldiversitywithearthtonguesphylogenetictestofsatealignmentsforenvironmentalitsdata AT francesclopezgiraldez tastingsoilfungaldiversitywithearthtonguesphylogenetictestofsatealignmentsforenvironmentalitsdata AT wenyingzhuang tastingsoilfungaldiversitywithearthtonguesphylogenetictestofsatealignmentsforenvironmentalitsdata AT yuchengdai tastingsoilfungaldiversitywithearthtonguesphylogenetictestofsatealignmentsforenvironmentalitsdata AT peterrjohnston tastingsoilfungaldiversitywithearthtonguesphylogenetictestofsatealignmentsforenvironmentalitsdata AT jeffreyptownsend tastingsoilfungaldiversitywithearthtonguesphylogenetictestofsatealignmentsforenvironmentalitsdata
_version_	1718424198063325184

Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.

Ejemplares similares