Research article
Identification and localisation of the NB-LRR gene family within the potato genome
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
BMC Genomics 2012, 13:75 doi:10.1186/1471-2164-13-75
Published: 15 February 2012Additional 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+.
Format: XLSX Size: 47KB Download file
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 *.
Format: EPS Size: 966KB Download file
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 *.
Format: EPS Size: 757KB Download file
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 *.
Format: EPS Size: 1.4MB Download file
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 *.
Format: EPS Size: 1.1MB Download file
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 *.
Format: EPS Size: 1.1MB Download file
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 *.
Format: EPS Size: 908KB Download file
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 *.
Format: EPS Size: 1MB Download file
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 *.
Format: EPS Size: 1.1MB Download file
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 *.
Format: EPS Size: 1007KB Download file
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 *.
Format: EPS Size: 1.3MB Download file
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 *.
Format: EPS Size: 1.2MB Download file
