Simultaneous pyrosequencing of the 16S rRNA, IncP-1 trfA, and merA genes.
The use of amplicon pyrosequencing makes it possible to produce thousands of sequences of the same gene at relatively low costs. Here we show that it is possible to simultaneously sequence the 16S rRNA gene, IncP-1 trfA gene and mercury reductase gene (merA) as a way for screening the diversity of several genes in the same samples. As a proof-of-concept two different soil samples and a wastewater sample were screened. Multiplexing identifiers (MIDs) and sequencing adapters were added to amplicons using a tailed PCR approach and the universal overhangs U1 and U2 for this approach were redesigned. Furthermore, this is the first time the IncP-1 plasmid diversity was studied by amplicon pyrosequencing and for this purpose a clustering threshold of 89% nucleotide sequence similarity was determined to differentiate the IncP-1 subgroups.
Section for Microbiology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark; Section for Microbiology, Universitetsparken 15, Building 1, DK-2100 Copenhagen OE, Denmark.
Peter N
PN
Holmsgaard
Søren J
SJ
Sørensen
Lars H
LH
Hansen
D001419:Bacteria / Q000145:classification / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification*; D005798:Genes, Bacterial; D010957:Plasmids / Q000235:genetics; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA / Q000379:methods*
D017931:DNA Primers; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
16S rRNA gene; Amplicon pyrosequencing; C; Collstrup site; IncP-1 trfA; Indels; Insertions and deletions; J; Jægersborg Hegn; MIDs; T(a); U-linker; W; Wastewater; annealing temperature; merA; multiplexing identifiers