Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group phureja

• Published in: PloS one Vol. 7; no. 4; p. e34775
• Main Authors: Lozano, Roberto, Ponce, Olga, Ramirez, Manuel, Mostajo, Nelly, Orjeda, Gisella
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 06.04.2012; Public Library of Science (PLoS)
• Subjects: Amino Acid Sequence; Analysis; Arabidopsis; Arabidopsis thaliana; Base Sequence; Binding Sites; Biology; Chromosome Mapping; Chromosomes; Chromosomes, Plant; Codons; Conserved Sequence; Disease resistance; Disease Resistance - genetics; Disease Resistance - immunology; Frameshift mutation; Gene mapping; Genes; Genome, Plant; Genome-Wide Association Study; Genomes; Genomics; Homology; Interleukin 1; Kinases; Leucine; Medicine; Molecular Sequence Data; Multigene Family; Mutation; Nonsense mutation; Nucleotides - metabolism; Phylogeny; Pinus monticola; Plant diseases; Plant Diseases - genetics; Plant Diseases - immunology; Plant Proteins - chemistry; Plant Proteins - genetics; Protein Binding; Protein Structure, Tertiary; Proteins - chemistry; Proteins - genetics; Pseudogenes; Pseudogenes - genetics; Sequence Homology, Amino Acid; Solanaceae; Solanum tuberosum; Solanum tuberosum - genetics; Viral infections
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0034775

The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising ∼41% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes.