Abstract
Tobacco (Nicotiana tabacum) is an important cash crop and an ideal experimental system for studies on plant–pathogen interaction. The sequenced tobacco genome provides an opportunity for examining resistance gene homologs (RGHs) in the tobacco genome. Thirty nucleotide-binding site-type RGHs were annotated from genomic data, and another 281 putative RGHs were identified via PCR amplification from wild and cultivated tobacco. The newly identified RGHs are similar to other known RGHs, and some were categorized into new groups or branches that are different from known Nicotiana R genes or RGHs. Of the 281RGHs, 146 were identified from a single tobacco genome. We did not find any polymorphism at the RGHs in cultivated accessions, implying that strong domestication selection and/or demographic effects might have caused a sharp reduction in nucleotide diversity. Three positive selection sites were found in several RGH groups, while purifying selection is pervasive in the RGH family. Our results provide a primary RGH pool and several positively selected sites for the further functional validation of resistance genes in tobacco.
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Abbreviations
- RGH:
-
resistance gene homolog
- RGA:
-
resistance gene analog
- NBS:
-
nucleotide-binding site
- R:
-
resistance
- LRR:
-
leucine-rich repeat
- TGI:
-
Tobacco Genome Initiative
- CC:
-
coiled-coil
- TIR:
-
Toll-IL-1 resistance
- EST:
-
expressed sequence tag
- BLAST:
-
basic local alignment search tool
- LRT:
-
likelihood ratio test
- BEB:
-
Bayes empirical Bayes
- SNP:
-
single nucleotide polymorphism
- RAPD:
-
random amplified polymorphic DNA
- AFLP:
-
amplified fragment length polymorphism
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Acknowledgements
This work was supported by the Yunnan Tobacco Company, which is affiliated with the China Tobacco Company (06A03). We thank Prof. Mingwei Gao (Zhejiang University) for his critical reading of the manuscript.
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Figure S1
PCR amplification gel for tobacco RGHs (DOC 25 kb)
Figure S2
Phylogenetic trees constructed by neighbor-joining methods based on the nucleotide sequences of tobacco RGH groups. A NBS226; B NBS173; C NBS271; D NBS374; E Nbs359; F NBS182; G NBS334; H NBS267; I NBS329 (DOC 40 kb)
Figure S3
Alignment of sequences containing the NBS domain of an RGH (NBS133) from wild and cultivated tobacco (DOC 393 kb)
Table S1
(DOC 53 kb)
Table S2
(DOC 31 kb)
Table S3
(DOC 30 kb)
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Leng, X., Xiao, B., Wang, S. et al. Identification of NBS-Type Resistance Gene Homologs in Tobacco Genome. Plant Mol Biol Rep 28, 152–161 (2010). https://doi.org/10.1007/s11105-009-0134-z
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DOI: https://doi.org/10.1007/s11105-009-0134-z