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Open Access Research article

Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops

Hongjian Wan12, Wei Yuan2, Kailiang Bo1, Jia Shen1, Xin Pang1 and Jinfeng Chen1*

Author Affiliations

1 State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China

2 Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People’s Republic of China

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BMC Genomics 2013, 14:109  doi:10.1186/1471-2164-14-109

Published: 19 February 2013

Additional files

Additional file 1:

Coding DNA and protein sequences of the NBS-encoding genes from cucumbers (Cucumis sativus L).

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Additional file 2:

Predicted domains of each NBS-encoding genes and numbers of LRR motifs in cucumber.

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Additional file 3:

Sequence identity between 9930 and Gy14 NBS-encoding genes.

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Additional file 4:

Distribution of the NBS-encoding genes with different numbers of introns in cucumber.

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Additional file 5:

Motif patterns of NBS-encoding genes in cucumbers (Cucumis sativusL.). (A) CC-NBS family (B) TIR-NBS family

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Additional file 6:

(A) Motif sequence logos in the cucumber CC-NBS family of NBS-encoding genes. (B) Motif sequence logos in the cucumber TIR-NBS family of NBS-encoding genes.

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Additional file 7:

PCR amplification products generated by the three selected resistance gene degenerate primers in the four major Cucurbitaceae crops.

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Additional file 8:

Phylogenetic comparison of Cucurbitaceae NBS-encoding genes and RGHs. The TIR- and CC-NBS families are distinct. The former is divided into subfamilies TIR1 to TIR 9 and the latter is separated into subfamilies CC1 to CC4.

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Additional file 9:

The detailed phylogenetic tree from Figure 4. The tree consists of 63 Cucurbitaceae and 52 Arabidopsis CC-NBS protein sequences. Parentheses indicate the ancient CC family (N1 to N4) as defined by Cannon et al. [41].

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Additional file 10:

The detailed phylogenetic tree from Figure 5. The tree consists of 152 Cucurbitaceae and 106 Arabidopsis TIR-NBS sequences. Arabidopsis subfamilies are indicated by At-TIR-NBS-A to At-TIR-NBS-G corresponding to the seven TIR subfamilies identified by Richly et al. [52].

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Additional file 11:

Total number of predicted NBS-encoding genes identified in the six sequenced angiosperm genomes. The values for Carica papaya, Arabidopsis thaliana, Vitis vinifera, Oryza sativa, and Populus trichocarpa were previously summarized by Yang et al. [37] and Porter et al. [48]. The total number of predicted protein encoding genes and the genome size of each species is also shown.

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Additional file 12:

Amino acid sequence alignment of NBS-encoding genes. The conserved domains are highlighted and indicated by an arrow. The alignment was constructed using Clustal X software.

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Additional file 13:

Degenerate primers used for PCR amplification from the four major Cucurbitaceae crops (melon, bottle gourd, luffa and watermelon).

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