Natural variation, functional divergence, and local adaptation of nucleotide binding site sequences in Rhododendron (Ericaceae)

Pei-Chun Liao, Jeng Der Chung, Chia Ling Chen, Chiun Jr Hwang, Ya Hsiu Sung, Yung-Ta Chang, Shih-Ying Hwang

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

To further understand natural variation and local adaptation in the evolution of plant defense, we analyzed polymorphism data of nucleotide-binding site (NBS) sequences of Rhododendron at both the species and population levels. Multiple duplication events were found in NBS sequence evolution in Rhododendron genomes, which resulted in six clades: A-F. Our results of several NBS clade pair comparisons showed significant evolutionary rate changes based on differences in substitution rates between NBS-encoding protein clades (type I functional divergence). Pairwise comparisons of NBS clades further revealed that many amino acids displayed radical biochemical property changes causing a shift in amino acid preferences between NBS-encoding protein clades (type II functional divergence). Such divergent evolution of NBSs is likely a consequence of positive selection related to differentiation of recognition signals in response to different pathogens. Primers specific to clades B and C, which differed in the number of radical amino acid changes causing type II functional divergence and levels of nucleotide diversities, were further used to amplify population clades B and C NBS sequences of Rhododendron formosanum populations. Higher levels of net nucleotide divergences (measured by D a) between R. formosanum populations were found based on NBS sequences of population clade B compared to population clade C, suggesting local adaptation of population clade B NBS sequences. Local adaptation can be further inferred for R. formosanum population clade B NBS sequences because of significant Φ ST based on variation in nonsynonymous substitutions. Furthermore, local adaptation was also suggested by no significant correlation of population pairwise F ST between population clades B and C in R. formosanum.

Original languageEnglish
Pages (from-to)879-893
Number of pages15
JournalTree Genetics and Genomes
Volume8
Issue number4
DOIs
Publication statusPublished - 2012 Aug 1

Fingerprint

Ericaceae
Rhododendron
local adaptation
binding sites
Nucleotides
divergence
nucleotides
Binding Sites
amino acid
substitution
Population
plant defense
protein
polymorphism
genome
pathogen
Amino Acids
amino acids
divergent evolution

Keywords

  • Functional divergence
  • Local adaptation
  • Nucleotide-binding-site domain
  • Positive selection
  • Rhododendron

ASJC Scopus subject areas

  • Forestry
  • Molecular Biology
  • Genetics
  • Horticulture

Cite this

Natural variation, functional divergence, and local adaptation of nucleotide binding site sequences in Rhododendron (Ericaceae). / Liao, Pei-Chun; Chung, Jeng Der; Chen, Chia Ling; Hwang, Chiun Jr; Sung, Ya Hsiu; Chang, Yung-Ta; Hwang, Shih-Ying.

In: Tree Genetics and Genomes, Vol. 8, No. 4, 01.08.2012, p. 879-893.

Research output: Contribution to journalArticle

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