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. 2025:2892:151-168.
doi: 10.1007/978-1-0716-4330-3_11.

Annotation of RxLR Effectors in Oomycete Genomes

Nicholas C Cauldron  1 , Martha A Sudermann  1 , Camilo H Parada-Rojas  1 , Niklaus J Grünwald  2
Affiliations

Annotation of RxLR Effectors in Oomycete Genomes

Nicholas C Cauldron et al. Methods Mol Biol. 2025.

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.

Keywords: EER; Effector; RxLR; Signal peptide.

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