Poster abstracts

Poster number 5 submitted by Benli Chai

The Ribosomal Databse Project: Tools and sequences for rRNA analysis.

Benli Chai (Ribosomal Database Project, Center for Microbial Ecology, Michigan State University), Jordan A. Fish (Ribosomal Database Project, Center for Microbial Ecology, Michigan State University), Qiong Wang (Ribosomal Database Project, Center for Microbial Ecology, Michigan State University), James M. Tiedje (Ribosomal Database Project, Center for Microbial Ecology, Michigan State University), James R. Cole (Ribosomal Database Project, Center for Microbial Ecology, Michigan State University)

Abstract:
The ribosomal RNA gene is the most important molecular marker for studying microbial phylogeny because of its universal nature and the presence of conserved sequence regions facilitating PCR primer design. The current high-throughput sequencing revolution has greatly expanded the use of rRNA in exploring and accurately cataloging microbial diversity in complex natural environments. The Ribosomal Database Project (RDP; http://rdp.cme.msu.edu) provides data and services for analyzing data derived from rRNA genes. With its analysis tool suite, private user workspace (myRDP), and monthly-updated database of aligned and annotated quality-controlled public rRNA sequences (1,921,179 as of September 2011), RDP is widely used by the microbial research community in studies of microbial ecology, evolution, environmental engineering, and in understanding the diversity of life. The RDP recently added fungal 28S rRNA gene reference sequences, along with a hand-vetted fungal taxonomy (kindly provided by C. R. Kuske, A. Porras-Alfaro and their co-workers). Fungi are important in health, food, and biogeochemical cycling. Fungal rRNA sequence can be rapidly placed into this fungal taxonomy by using the RDP Classifier, an implementation of a Naïve Baysian machine learning algorithm. The RDP Classifier is already a standard tool for high-throughput bacterial rRNA sequence taxonomic assignment. In addition, the RDP Pyrosequencing Pipeline offers an easy-to-use web-based tool suite to automate computationally intensive analyzing tasks. The Pipeline takes raw reads through initial processing steps to hierarchical clustering into OTUs or taxonomic assignment using the RDP Classifier. Several common ecological metrics are provided, including Chao1, Shannon Index and rarefaction. Results are made available in formats suitable for common statistical and ecological packages. Other RDP tools include Sequence Match for finding nearest neighbors; Library Compare for determining differentially represented taxa between two libraries; RDP Probe Match for determining taxonomic coverage of primers and probes; Tree Builder for rapid phylogenetic tree construction; and Browsers that provide entry to the public sequences.

Keywords: rRNA, pyrosequencing, phylogeny