High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples.
Mycorrhiza
; 22(4): 309-15, 2012 May.
Article
in En
| MEDLINE
| ID: mdl-21779811
ABSTRACT
In this methodological study, we compare 454 sequencing and a conventional cloning and Sanger sequencing approach in their ability to characterize fungal communities PCR amplified from four root systems of the ectomycorrhizal plant Bistorta vivipara. To examine variation introduced by stochastic processes during the laboratory work, we replicated all analyses using two independently obtained DNA extractions from the same root systems. The ITS1 region was used as DNA barcode and the sequences were clustered into OTUs as proxies for species using single linkage clustering (BLASTC lust) and 97% sequence similarity cut-off. A relatively low overlap in fungal OTUs was observed between the 454 and the clone library datasets - even among the most abundant OTUs. In a non-metric multidimensional scaling analysis, the samples grouped more according to methodology compared to plant. Some OTUs frequently detected by 454, most notably those OTUs with taxonomic affinity to Glomales, were not detected in the Sanger dataset. Likewise, a few OTUs, including Cenococcum sp., only appeared in the clone libraries. Surprisingly, we observed a significant relationship between GC/AT content of the OTUs and their proportional abundances in the 454 versus the clone library datasets. Reassuringly, a very good consistency in OTU recovery was observed between replicate runs of both sequencing methods. This indicates that stochastic processes had little impact when applying the same sequencing technique on replicate samples.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
DNA, Fungal
/
Sequence Analysis, DNA
/
Plant Roots
/
Polygonaceae
/
Mycorrhizae
Type of study:
Evaluation_studies
Language:
En
Journal:
Mycorrhiza
Journal subject:
BIOLOGIA
Year:
2012
Document type:
Article
Affiliation country:
Norway