@ARTICLE{TreeBASE2Ref17308,
author = {Martin Ryberg and R. H. Nilsson and Erik Kristiansson and Mats T?pel and Stig Jacobsson and Ellen Larsson},
title = {Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota)},
year = {2008},
keywords = {},
doi = {10.1186/1471-2148-8-50},
url = {},
pmid = {18282272},
journal = {BMC Evolutionary biology},
volume = {8},
number = {},
pages = {50},
abstract = {Background: The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe were retrieved from GenBank and divided into species that were identified in a phylogenetic context through a reference dataset from an ongoing study of the genus. Sequence metadata stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to other mycorrhizal genera. Results: Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences accounts for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution. Conclusions: Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.}
}
Citation for Study 1978
Citation title:
"Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota)".
This study was previously identified under the legacy study ID S1968
(Status: Published).
Citation
Ryberg M., Nilsson R., Kristiansson E., T?pel M., Jacobsson S., & Larsson E. 2008. Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota). BMC Evolutionary biology, 8: 50.
Authors
-
Ryberg M.
-
Nilsson R.
-
Kristiansson E.
-
T?pel M.
-
Jacobsson S.
-
Larsson E.
Abstract
Background: The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe were retrieved from GenBank and divided into species that were identified in a phylogenetic context through a reference dataset from an ongoing study of the genus. Sequence metadata stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to other mycorrhizal genera. Results: Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences accounts for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution. Conclusions: Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.
External links
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- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S1978
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- Show BibTeX reference
@ARTICLE{TreeBASE2Ref17308,
author = {Martin Ryberg and R. H. Nilsson and Erik Kristiansson and Mats T?pel and Stig Jacobsson and Ellen Larsson},
title = {Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota)},
year = {2008},
keywords = {},
doi = {10.1186/1471-2148-8-50},
url = {},
pmid = {18282272},
journal = {BMC Evolutionary biology},
volume = {8},
number = {},
pages = {50},
abstract = {Background: The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe were retrieved from GenBank and divided into species that were identified in a phylogenetic context through a reference dataset from an ongoing study of the genus. Sequence metadata stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to other mycorrhizal genera. Results: Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences accounts for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution. Conclusions: Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.}
}
- Show RIS reference
TY - JOUR
ID - 17308
AU - Ryberg,Martin
AU - Nilsson,R. H.
AU - Kristiansson,Erik
AU - T?pel,Mats
AU - Jacobsson,Stig
AU - Larsson,Ellen
T1 - Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota)
PY - 2008
KW -
UR -
N2 - Background: The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe were retrieved from GenBank and divided into species that were identified in a phylogenetic context through a reference dataset from an ongoing study of the genus. Sequence metadata stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to other mycorrhizal genera. Results: Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences accounts for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution. Conclusions: Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.
L3 - 10.1186/1471-2148-8-50
JF - BMC Evolutionary biology
VL - 8
IS -
ER -
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