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

Tools

Jupe, Florian and Pritchard, Leighton and Etherington, Graham J and MacKenzie, Katrin and Cock, Peter JA and Wright, Frank and Sharma, Sanjeev Kumar and Bolser, Dan and Bryan, Glenn J and Jones, Jonathan DG and Hein, Ingo (2012) Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics, 13. 75. ISSN 1471-2164 (https://doi.org/10.1186/1471-2164-13-75)

[thumbnail of Jupe-etal-BMC-Genomics-2012-Identification-and-localisation-of-the-NB-LRR-gene-family]
Preview
 Text. Filename: Jupe_etal_BMC_Genomics_2012_Identification_and_localisation_of_the_NB_LRR_gene_family.pdf
Final Published Version
License: Creative Commons Attribution 3.0 logo
Download (1MB)| Preview

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.

ORCID iDs

Jupe, Florian, Pritchard, Leighton ORCID logoORCID: https://orcid.org/0000-0002-8392-2822, Etherington, Graham J, MacKenzie, Katrin, Cock, Peter JA ORCID logoORCID: https://orcid.org/0000-0001-9513-9993, Wright, Frank, Sharma, Sanjeev Kumar, Bolser, Dan, Bryan, Glenn J, Jones, Jonathan DG and Hein, Ingo;
CORE (COnnecting REpositories)