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Properties of group-specific primer pairs and their coverage for phylogenetic and environmental groups.

By John Christian Gaby (148535) and Daniel H. Buckley (51969)

Abstract

a<p>Data indicate primer binding to specific groupings in the <i>nifH</i> phylogeny. Abbreviations are as follows: <i>Alpha, Beta, and Gamma Proteobacteria</i> (<b>Pr</b>); <i>Cyanobacteria</i> (<b>Cy</b>); Cluster III (<b>III</b>); Cluster IA (<b>IA</b>); <i>Paenibacillus</i> (<b>Pb</b>); <i>Frankia</i> (<b>Fr</b>); <i>Epsilon Proteobacteria</i> Containing Cluster (<b>Ep</b>); paralogous sequences in Cluster IV (<b>IV</b>). In some cases highly degenerate primers bind to multiple positions in the sequence generating coverage values that exceed 100%.</p>b<p>Primer coverage queried against sequences recovered from specific environments (Environ.) as described in methods. Environments include: soils (<b>Soil</b>), microbial mats (<b>Mat</b>), and pelagic marine samples (<b>Sea</b>).</p>c<p>Position of amplicon in <i>nifH</i> is relative to <i>A. vinelandii nifH</i> (Genbank ACCN# M20568).</p>d<p>Length expected for PCR amplicon.</p>e<p>Data indicate primer binding with 0 mismatches to all <i>nifH</i> sequences in the database.</p>f<p>This binding position for the reverse primer sequence lies beyond the stop codon of <i>Frankia</i> sp. (Genbank ACCN# M21132) and cannot be represented using the <i>A. vinelandii</i> numbering system.</p><p>NA Data not available as nucleotide information is not available for the target group in the region of primer binding.</p

Topics: Biochemistry, Microbiology, group-specific, primer, pairs, phylogenetic
Year: 2012
DOI identifier: 10.1371/journal.pone.0042149.t005
OAI identifier: oai:figshare.com:article/274200
Provided by: FigShare
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