| 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. | |
| | |
MedLine Citation:
|
PMID: 20636324 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
• Compared with Sanger sequencing-based methods, pyrosequencing provides orders of magnitude more data on the diversity of organisms in their natural habitat, but its technological biases and relative accuracy remain poorly understood. • This study compares the performance of pyrosequencing and traditional sequencing for species' recovery of ectomycorrhizal fungi on root tips in a Cameroonian rain forest and addresses biases related to multi-template PCR and pyrosequencing analyses. • Pyrosequencing and the traditional method yielded qualitatively similar results, but there were slight, but significant, differences that affected the taxonomic view of the fungal community. We found that most pyrosequencing singletons were artifactual and contained a strongly elevated proportion of insertions compared with natural intra- and interspecific variation. The alternative primers, DNA extraction methods and PCR replicates strongly influenced the richness and community composition as recovered by pyrosequencing. • Pyrosequencing offers a powerful alternative for the identification of ectomycorrhizal fungi in pooled root samples, but requires careful selection of molecular tools. A well-populated backbone database facilitates the detection of biological and technical artifacts. The pyrosequencing pipeline is available at http://unite.ut.ee/454pipeline.tgz. |
| | |
Authors:
|
Leho Tedersoo; R Henrik Nilsson; Kessy Abarenkov; Teele Jairus; Ave Sadam; Irja Saar; Mohammad Bahram; Eneke Bechem; George Chuyong; Urmas Kõljalg |
Related Documents
:
|
12881164 - An associative model of rat serial pattern learning in three-element sequences. 12169214 - Conversion of nucleotides sequences into genomic signals. 16452804 - A block coding method that leads to significantly lower entropy values for the proteins... 17153954 - Video compression using spatiotemporal regularity flow. 10713344 - Molecular cloning and sequencing of the low-affinity ige receptor (cd23) for horse and ... 20621844 - Comparative genomic and phylogenetic investigation of the xenobiotic metabolizing aryla... |
Publication Detail:
|
Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2010-07-15 |
Journal Detail:
|
Title: The New phytologist Volume: 188 ISSN: 1469-8137 ISO Abbreviation: New Phytol. Publication Date: 2010 Oct |
Date Detail:
|
Created Date: 2010-09-15 Completed Date: 2011-01-05 Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 9882884 Medline TA: New Phytol Country: England |
Other Details:
|
Languages: eng Pagination: 291-301 Citation Subset: IM |
Affiliation:
|
Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia. leho.tedersoo@ut.ee |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Amino Acid Substitution
/
genetics Bias (Epidemiology) DNA Barcoding, Taxonomic DNA, Intergenic / genetics Mycorrhizae / genetics* Reproducibility of Results Sequence Analysis, DNA / methods* Temperature* Tropical Climate* |
| Chemical | |
Reg. No./Substance:
|
0/DNA, Intergenic |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: The Pseudomonas syringae effector protein HopZ1a suppresses effector-triggered immunity.
Next Document: Expression of Ten-m/Odz3 in the fibrous layer of mandibular condylar cartilage during postnatal grow...