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

Additional files

Additional file 1:

Gene bank (NCBI) accession numbers for proteins used in the positive and negative training sets. 'Positive' NB-LRR and 'negative' non-NB-LRR sequence training sets were used with the MEME Suite psp-gen script (version 4.4.0) [56] to identify discriminative motifs from the positive set.

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Additional file 2:

Graphical MAST search output. Graphical overview of the MAST search output ranked according to the E-value scores obtained for MEME motifs. By including DMPs that yielded an E-value score of up to 2.0, 765 proteins were identified. Within the E-value range of the negative training set, 87 sequences encoded for very short DMPs and contained additional NB-LRR gene associated domains in the extended DMP+ sequence.

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Additional file 3:

List of identified DM NB-LRR genes. Identified NB-LRR genes are listed, together with information on their PGSC identity, coding DNA strand, annotation, number of identified open reading frames (ORFs), the predicted pseudomolecule (LG), start of original DMG on LG, end of original DMG on LG, repeat density, gene density, and motif complement of the annotated sequence DMG+.

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Additional file 4:

FASTA sequences for the re-annotated DM NB-LRR coding sequences and the conceptual translations. This file contains the re-annotated coding sequences for identified DM NB-LRR genes, as well as the derived amino acid translation. IDs correspond to the original DMG identifiers provided by the PGSC.

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Additional file 5:

Comparison of functionally characterised Solanaceae R genes to DM NB-LRR cds. E-values, pairwise identity and coverage were established using BLASTP. The chromosome and cluster positions are shown alongside the phylogenetic group information.

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Additional file 6:

Detailed phylogenetic analysis of the DM NB-LRR NB-ARC domains. The NB-ARC domains of TNL and CNL type gene products were used, alongside selected NB-ARC domains from functional resistance genes, to study the phylogenetic relationships between them.

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Additional file 7:

Detailed view of potato chromosome 1. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 8:

Detailed view of potato chromosome 2. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 9:

Detailed view of potato chromosome 3. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 10:

Detailed view of potato chromosome 4. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 11:

Detailed view of potato chromosome 5. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 12:

Detailed view of potato chromosome 6. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 13:

Detailed view of potato chromosome 7. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 14:

Detailed view of potato chromosome 8. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 15:

Detailed view of potato chromosome 9. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 16:

Detailed view of potato chromosome 10. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 17:

Detailed view of potato chromosome 11. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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Additional file 18:

Detailed view of potato chromosome 12. Genes encoded by the positive DNA strand are depicted on the left hand side of the chromosome, whereas those encoded by the negative strand are shown on the right. NB-LRR genes belonging to clusters are indicated by vertical bars. Heterogeneous clusters are indicated by an *.

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