Poster: Molecular & Cellular Plant-Microbe Interactions: MPMI
MetacodeR: An R package for comparative analysis and visualization of microbial communities and evaluation of metabarcoding primer specificity
Z. FOSTER (1), N. Grunwald (1) (1) USDA Agricultural Research Service / Oregon State University, U.S.A.
Metabarcoding, the sequencing of a locus amplified from environmental DNA, is revealing the unculturable majority of microbes for the first time, but new methods present new challenges. Complex hierarchical data are difficult to plot and the commonly used stacked bar charts are ineffective when plotting multiple taxonomic ranks or treatments. In addition, the choices of loci and barcode primers are a source of underexplored bias. MetacodeR is a new tool kit for metabarcoding and community ecology, focusing on visualization of taxonomic data and in silico primer/barcode evaluation. It provides tools to integrate quantitative data from thousands of taxa and multiple communities into intuitive tree-based plots. Data from one or more communities are mapped to tree element size or color, as in a heat map. This allows for rapid exploration of data and information-rich, publication-quality graphics. In addition, metacodeR provides critical tools for evaluating potential primers and barcode loci. In silico PCR evaluates primer specificity and barcode gap analysis estimates error rates and resolution. MetacodeR is currently being applied to evaluating the diversity of fungi and oomycetes in the rhizosphere of nursery-grown rhododendron. The ability to easily test new primers/barcodes will accelerate the adoption of metabarcoding to emerging or understudied pathogen groups, such as oomycetes, and intuitive plotting will make subtle patterns in complex data more apparent.