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Open Access Highly Accessed Research article

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

Florian Jupe12, Leighton Pritchard3, Graham J Etherington2, Katrin MacKenzie4, Peter JA Cock3, Frank Wright4, Sanjeev Kumar Sharma1, Dan Bolser5, Glenn J Bryan1, Jonathan DG Jones2 and Ingo Hein1*

Author Affiliations

1 Cell and Molecular Sciences, The James Hutton Institute (JHI), Dundee, DD2 5DA, UK

2 The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK

3 Information and Computational Sciences, The James Hutton Institute, UK

4 Biomathematics and Statistics Scotland (BioSS), The James Hutton Institute, UK

5 University of Dundee, College of Life Sciences, Dundee, DD1 5EH, UK

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BMC Genomics 2012, 13:75  doi:10.1186/1471-2164-13-75

Published: 15 February 2012

Abstract

Background

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.

Results

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.

Conclusions

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.