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Annotation of RxLR Effectors in Oomycete Genomes
Nicholas C Cauldron1, Martha A Sudermann1, Camilo H Parada-Rojas1
1Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
Abstract:
Pathogens have evolved effector proteins to suppress host immunity and facilitate plant infections. RxLR effectors are small, secreted effector proteins with conserved RxLR and dEER amino acid motifs at the N terminus and highly variable C termini and are commonly found in oomycete species. We provide computational approaches to annotate RxLR candidate effector genes in a genome assembly in FASTA format with an available GFF file. Hidden Markov Modeling (HHM) is used in combination with regular expressions to search for RxLR and EER amino acid patterns.
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