Molecular evolution of a family of resistance gene analogs of nucleotide-binding site sequences in Solanum lycopersicum

Pei-Chun Liao, Kuan Hung Lin, Chin Ling Ko, Shih-Ying Hwang

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Nucleotide-binding site-leucine-rich repeats (NBS-LRR) gene families are one of the major plant resistance genes. Genomic NBS evolution was studied in many plant species for diverse arrays of NBS gene families. In this study, we focused on one family of NBS sequences in an attempt to understand how closely related NBS sequences evolved in the light of selection in domesticated plant species. A phylogenetic analysis revealed five major clades (A-E) and five subclades (A1-A5) within clade A of cloned NBS sequences. Positive selection was only detected in newly evolved NBS lineages in subclades of clade A. Positively selected codon sites were found among NBS sequences of clade A. A sliding-window analysis revealed that regions with Ka/Ks ratios of >1 were in the inter-motifs when paired clades were compared, but regions with Ka/Ks ratios of >1 were found across NBS sequences when subclades of clade A were compared. Our results based on a family of closely related NBS sequences showed that positive selection was first exerted on specific lineages across all NBS sequences after selective constraints. Subsequently, sequences with mutations in commonly conserved motifs were scrutinized by purifying selection. In the long term, conserved high frequency alleles in commonly conserved motifs and changes in inter-motifs were maintained in the investigated family of NBS sequences. Moreover, codons identified to be under positive selection in the inter-motifs were mainly located in regions involved in functions of ATP binding or hydrolysis.

Original languageEnglish
Pages (from-to)1229-1240
Number of pages12
JournalGenetica
Volume139
Issue number10
DOIs
Publication statusPublished - 2011 Oct 1

Fingerprint

Molecular Evolution
Solanum lycopersicum
Lycopersicon esculentum
Codon
binding sites
Nucleotides
nucleotides
Binding Sites
codons
Plant Genes
Gene Frequency
Leucine
Genes
Hydrolysis
genes
Adenosine Triphosphate
Mutation
leucine
gene frequency
hydrolysis

Keywords

  • NBS sequences
  • Positive selection
  • Resistance gene analogs
  • Solanum lycopersicum

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics
  • Plant Science
  • Insect Science

Cite this

Molecular evolution of a family of resistance gene analogs of nucleotide-binding site sequences in Solanum lycopersicum. / Liao, Pei-Chun; Lin, Kuan Hung; Ko, Chin Ling; Hwang, Shih-Ying.

In: Genetica, Vol. 139, No. 10, 01.10.2011, p. 1229-1240.

Research output: Contribution to journalArticle

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