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Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns

Hongjian Wan, Wei Yuan, Qingjing Ye, Rongqing Wang, Meiying Ruan, Zhimiao Li, Guozhi Zhou, Zhuping Yao, Jing Zhao, Shujun Liu and Yuejian Yang*

Author Affiliations

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

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BMC Genomics 2012, 13:502  doi:10.1186/1471-2164-13-502

Published: 21 September 2012

Additional files

Additional file 1:

PCR amplification products generated by two pairs of degenerate primers in pepper. Lanes A and B were products of the primer combinations Ploop-1 and GLPL-1 and Ploop-2 and GLPL-2, respectively; M: marker 2000.

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Additional file 2:

DNA and protein sequences of the CaRGAs in pepper.

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Additional file 3:

Site-specific profile of predicted critical amino acid residues responsible for the functional divergence between the non-TIR and TIR-NBS RGA subfamilies, measured at each site using the posterior probability of being associated with functional divergence. The arrows point to 13 amino acid residues at which functional divergence between the two subfamilies was predicted.

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Additional file 4:

Illustration of specificity-determining positions (SDPs) in the non-TIR-and TIR-NBS-LRR subfamilies in pepper. ‘−’ indicates gaps in the alignment. Possible SDPs that might determine functional specificity are highlighted in red and indicated by arrows.

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Additional file 5:

(A) Degenerate primer sequences used in DNA amplification of NBS-LRR CaRGAs from pepper. (B) qRT-PCR amplification was used to determine the expression profiles of cloned CaRGAs using the corresponding CaRGA-specific primers.

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