Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.

ABSTRACT: Microbial community profiling using 16S rRNA gene sequences requires accurate taxonomy assignments. 'Universal' primers target conserved sequences and amplify sequences from many taxa, but they provide variable coverage of different environments, and regions of the rRNA gene differ in taxonomic informativeness--especially when high-throughput short-read sequencing technologies (for example, 454 and Illumina) are used. We introduce a new evaluation procedure that provides an improved measure of expected taxonomic precision when classifying environmental sequence reads from a given primer. Applying this measure to thousands of combinations of primers and read lengths, simulating single-ended and paired-end sequencing, reveals that these choices greatly affect taxonomic informativeness. The m

SUBMITTER: Soergel DA 

PROVIDER: S-EPMC3379642 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature