Nucleotide-binding leucine-rich repeat (NLRs) receptors are involved in the intracellular recognition of pathogen effectors. Hundreds of genes encode these NLRs, and the genes are highly polymorphic. So far, a limited number of NLRs were characterized, and three mechanisms of effector recognition have been reported. However, there could be additional mechanisms that operate in the plants which can be studied only if the complete NLRome is decoded. NLR sequence enrichment and long-read sequencing (SMRT RenSeq) of 65 diverse Arabidopsis thaliana accessions identified 13167 NLR genes. Approximately 5% of the genes had at least one additional integrated protein domain (ID). Several IDs were found to be novel as compared to Col-0 reference, and this exposes the largely unexplored repertoires of NLR-IDs in Arabidopsis. Functional characterization of these IDs would provide insights into the different mechanisms underlying the recognition of effectors. The work thus provides a blueprint for investigating the NLRome in other plant species. bioRxiv 10.1101/537001