Environmental Oomycetes ITS1

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 of irrigation water samples from Oregon:

Redekar et al. (2019) Diversity of Phytophthora, Pythium, and Phytopythium species in recycled irrigation water in a container nursery. https://doi.org/10.1094/PBIOMES-10-18-0043-R

Different PCR primers were used to cover Pythium and Phytopythium as well as Phytophthora. This requires a new database of markers.

• Marker data
• Pipeline with defaults
• Different primers
• Building a custom database
• Specifying custom primers
• Examining the database
• Pipeline with custom database