Identification and localisation of the NB-LRR gene family within the potato genome

• Published in: BMC genomics Vol. 13; no. 1; p. 75
• Main Authors: Jupe, Florian, Pritchard, Leighton, Etherington, Graham J, Mackenzie, Katrin, Cock, Peter J A, Wright, Frank, Sharma, Sanjeev Kumar, Bolser, Dan, Bryan, Glenn J, Jones, Jonathan D G, Hein, Ingo
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 15.02.2012; BioMed Central; BMC
• Subjects: Amino Acid Motifs; Amino Acid Sequence; Cell receptors; Chromosome Mapping; Cluster Analysis; DNA sequencing; Genetic aspects; Genome, Plant; Leucine - chemistry; Molecular Sequence Data; Nucleotide sequencing; Physiological aspects; Plant Proteins - analysis; Plant Proteins - genetics; Potatoes; Solanum tuberosum - classification; Solanum tuberosum - genetics; United Kingdom
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-13-75

The potato genome sequence derived from the Solanum tuberosum Group Phureja clone DM1-3 516 R44 provides unparalleled insight into the genome composition and organisation of this important crop. A key class of genes that comprises the vast majority of plant resistance (R) genes contains a nucleotide-binding and leucine-rich repeat domain, and is collectively known as NB-LRRs. As part of an effort to accelerate the process of functional R gene isolation, we performed an amino acid motif based search of the annotated potato genome and identified 438 NB-LRR type genes among the ~39,000 potato gene models. Of the predicted genes, 77 contain an N-terminal toll/interleukin 1 receptor (TIR)-like domain, and 107 of the remaining 361 non-TIR genes contain an N-terminal coiled-coil (CC) domain. Physical map positions were established for 370 predicted NB-LRR genes across all 12 potato chromosomes. The majority of NB-LRRs are physically organised within 63 identified clusters, of which 50 are homogeneous in that they contain NB-LRRs derived from a recent common ancestor. By establishing the phylogenetic and positional relationship of potato NB-LRRs, our analysis offers significant insight into the evolution of potato R genes. Furthermore, the data provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from Solanum species.