title: Identification and distribution of the NBS-LRR gene family in the Cassava genome.
abstract: BACKGROUND
  Plant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analysing the genomic organization of resistance genes in this crop.
  
  
  RESULTS
  With searches for Pfam domains and manual curation of the cassava gene annotations, we identified 228 NBS-LRR type genes and 99 partial NBS genes. These represent almost 1% of the total predicted genes and show high sequence similarity to proteins from other plant species. Furthermore, 34 contained an N-terminal toll/interleukin (TIR)-like domain, and 128 contained an N-terminal coiled-coil (CC) domain. 63% of the 327 R genes occurred in 39 clusters on the chromosomes. These clusters are mostly homogeneous, containing NBS-LRRs derived from a recent common ancestor.
  
  
  CONCLUSIONS
  This study provides insight into the evolution of NBS-LRR genes in the cassava genome; the phylogenetic and mapping information may aid efforts to further characterize the function of these predicted R genes.
authors.affiliation: Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA. rjl278@cornell.edu.
authors.forename: Roberto
authors.initials: R
authors.lastname: Lozano
authors.affiliation: Institute for Genomic Diversity, Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA. mth3@cornell.edu.
authors.forename: Martha T
authors.initials: MT
authors.lastname: Hamblin
authors.affiliation: US Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA. seprochnik@lbl.gov.
authors.forename: Simon
authors.initials: S
authors.lastname: Prochnik
authors.affiliation: Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA. jj332@cornell.edu.|United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA. jj332@cornell.edu.
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Jannink
mesh_terms: D002874:Chromosome Mapping; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D054884:Host-Pathogen Interactions / Q000235:genetics; D002365:Manihot / Q000235:genetics* / Q000382:microbiology; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D053532:Xanthomonas axonopodis / Q000472:pathogenicity
chemical_list: D010940:Plant Proteins