- This repository contains scripts to analyze oomycete genomes for WY effector prediction and characterization, specifically focusing on the causal agent of lettuce downy mildew, Bremia lactucae.
Paper on BioRxiv: Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif
Kelsey Wood, Munir Nur, Juliana Gil, Kyle Fletcher, Kim Lakeman, Ayumi Gothberg, Tina Khuu, Jennifer Kopetzky, Archana Pandya, Mathieu Pel, Richard Michelmore
Supplemental motif table with all secreted genes, annotated with GeneID, sequence, species, and RXLR/EER/WY motif presence
Notes on the pipeline:
- RXLR string searches were done on non-redundant secretomes with cleaved sequences, yes the CSV above contains the full sequences for completeness.
- The ORFs folder contains the starting sequences of our pipeline, which were used as input to SignalP v4.1 (sensitive mode) to acquire secretomes and cleaved sequences and CD-HIT to reduce sequence redundancy