Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.

ABSTRACT: Targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. Vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. The overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknown diversity. To illustrate current issues surrounding amplicon read processing we provide examples for three ecofunctional gene groups. A combination of in silico, environmental and cultured strain sequences was used to test new primers targeting the dioxin and dibenzofuran degrading genes dxnA1, db

SUBMITTER: Penton CR 

PROVIDER: S-EPMC3775264 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature