Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.

ABSTRACT: High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer p

SUBMITTER: Hugerth LW 

PROVIDER: S-EPMC3995771 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature