Oomycete ITS1 & rps10

The first worked example looked at Phytophthora ITS1 data from woody-host trees, using the same PCR primers as the THAPBI PICT defaults, and the default database of Phytophthora ITS1 data provided.

Here we re-analyse a published dataset from a different group, doing Illumina MiSeq ITS1 amplicon sequencing as a base-line to evaluate a mitochondrial 40S ribosomal protein S10 (rps10) gene based marker as an alternative barcode for the wider group of oomycetes:

Foster et al. (2021) A New Oomycete Metabarcoding Method Using the rps10 Gene. https://doi.org/10.1094/PBIOMES-02-22-0009-R

The example combines our default Phytophthora focused ITS1 database with their broader rps10 reference sequences to process both markers together.

• Marker data
• Pipeline with custom database