4.4. Genome annotation

Genome annotation

Protein-coding genes were identified using MAKER pipeline⁶², and subjected to manual correction using an in-house script (HiCESAP). Gene structures were annotated using the gene search Augustus^63,64, GeneMark-ES⁶⁵ and SNAP⁶⁶. Protein family and orthologue clustering were performed using TribeMCL⁶⁷ and OrthoMCL⁶⁸ (BLASTP, E<=1e-10). Protein domains were assigned based on sequence homology or Pfam domains with scores greater than the trusted cutoff scores⁶⁹. Predicted gene function models were submitted to GO⁷⁰, KEGG, Swissprot, TrEmbl and Interpro. Gene categories were searched in NCBI COG and KOG databases using BLASTP (E<=1e-10) and transitively assigning functional categories. tRNA-scanSE and Rfam were for RNA predicting. Gene families, such as CRN proteins, NPP1-like proteins, elicitin-like proteins, small secreted cysteine-rich proteins (SCRs), and transporters were for manual review. Several bioinformatics strategies were employed for identification of candidate effectors on matches to a hidden Markov model (HMM) profile.