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

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 seq...

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Bibliographic Details
Published in:PloS one 2012-04, Vol.7 (4), p.e34775-e34775
Main Authors: Lozano, Roberto, Ponce, Olga, Ramirez, Manuel, Mostajo, Nelly, Orjeda, Gisella
Format: Article
Language:English
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
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0034775