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. 2020 Mar 20;11(3):333.
doi: 10.3390/genes11030333.

NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification

Nicholas Toda  1 , Camille Rustenholz  2 , Agnès Baud  3 , Marie-Christine Le Paslier  1 , Joelle Amselem  3 , Didier Merdinoglu  2 , Patricia Faivre-Rampant  1
Affiliations

NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification

Nicholas Toda et al. Genes (Basel). .

Abstract

Although there are a number of bioinformatic tools to identify plant nucleotide-binding leucine-rich repeat (NLR) disease resistance genes based on conserved protein sequences, only a few of these tools have attempted to identify disease resistance genes that have not been annotated in the genome. The overall goal of the NLGenomeSweeper pipeline is to annotate NLR disease resistance genes, including RPW8, in the genome assembly with high specificity and a focus on complete functional genes. This is based on the identification of the complete NB-ARC domain, the most conserved domain of NLR genes, using the BLAST suite. In this way, the tool has a high specificity for complete genes and relatively intact pseudogenes. The tool returns all candidate NLR gene locations as well as InterProScan ORF and domain annotations for manual curation of the gene structure.

Keywords: NLR disease resistance genes; NLR-Parser; functional annotation.

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Conflict of interest statement

Patricia Faivre-Rampant is Co-Guest Editor of a Special Issue of Genes, “NLR Gene Evolution in Plants”.

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