title: Genome-wide identification and mapping of NBS-encoding resistance genes in Solanum tuberosum group phureja.
abstract: 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.
authors.affiliation: Genomics Research Unit, Faculty of Sciences and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: Roberto
authors.initials: R
authors.lastname: Lozano
authors.forename: Olga
authors.initials: O
authors.lastname: Ponce
authors.forename: Manuel
authors.initials: M
authors.lastname: Ramirez
authors.forename: Nelly
authors.initials: N
authors.lastname: Mostajo
authors.forename: Gisella
authors.initials: G
authors.lastname: Orjeda
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D017124:Conserved Sequence; D060467:Disease Resistance / Q000235:genetics* / Q000276:immunology; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D000090263:Leucine-Rich Repeat Proteins; D008969:Molecular Sequence Data; D005810:Multigene Family; D009711:Nucleotides / Q000378:metabolism; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D011544:Pseudogenes / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D011198:Solanum tuberosum / Q000235:genetics*
chemical_list: D000090263:Leucine-Rich Repeat Proteins; D009711:Nucleotides; D010940:Plant Proteins; D011506:Proteins