Identification of NBS-Type Resistance Gene Homologs in Tobacco Genome

  • Xiaodong Leng
  • Bingguang Xiao
  • Sheng Wang
  • Yijie Gui
  • Yu Wang
  • Xiuping Lu
  • Jiahua Xie
  • Yongping Li
  • Longjiang Fan
Article

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.

Keywords

Nicotiana tabacum Resistance gene homolog (RGH) Resistance gene analog (RGA) Positive selection Genetic diversity 

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

Supplementary material

11105_2009_134_MOESM1_ESM.doc (24 kb)
Figure S1PCR amplification gel for tobacco RGHs (DOC 25 kb)
11105_2009_134_MOESM2_ESM.doc (40 kb)
Figure S2Phylogenetic 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)
11105_2009_134_MOESM3_ESM.doc (384 kb)
Figure S3Alignment of sequences containing the NBS domain of an RGH (NBS133) from wild and cultivated tobacco (DOC 393 kb)
11105_2009_134_MOESM4_ESM.doc (52 kb)
Table S1(DOC 53 kb)
11105_2009_134_MOESM5_ESM.doc (30 kb)
Table S2(DOC 31 kb)
11105_2009_134_MOESM6_ESM.doc (30 kb)
Table S3(DOC 30 kb)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Xiaodong Leng
    • 1
    • 2
  • Bingguang Xiao
    • 2
  • Sheng Wang
    • 1
  • Yijie Gui
    • 1
  • Yu Wang
    • 1
  • Xiuping Lu
    • 2
  • Jiahua Xie
    • 3
  • Yongping Li
    • 2
  • Longjiang Fan
    • 1
  1. 1.Institute of Crop ScienceZhejiang UniversityHangzhouChina
  2. 2.Joint Laboratory of Tobacco BioinformaticsYunnan Institute of Tobacco ScienceYuxiChina
  3. 3.Department of Pharmaceutical SciencesNorth Carolina Central UniversityDurhamUSA

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