An empirical demonstration of using pentatricopeptide repeat (PPR) genes as plant phylogenetic tools: Phylogeny of Verbenaceae and the Verbena complex

Yao Wu Yuan, Chang Liu, Hannah E. Marx, Richard G. Olmstead

Research output: Contribution to journalArticle

28 Scopus citations

Abstract

The pentatricopeptide repeat (PPR) gene family, with hundreds of members in land plant genomes, has been recognized as a tremendous resource for plant phylogenetic studies based on publicly available genomic data from model organisms. However, whether this appealing nuclear gene marker system can be readily applied to non-model organisms remains questionable, particularly given the potential uncertainties in designing specific primers to only amplify the locus of interest from the sea of PPR genes. Here we demonstrate empirically the use of PPR genes in the family Verbenaceae and the Verbena complex. We also lay out a general scheme to design locus-specific primers to amplify and sequence PPR genes in non-model organisms. Intergeneric relationships within the family Verbenaceae were fully resolved with strong support. Relationships among the closely related genera within the Verbena complex and among some species groups within each genus were also well resolved, but resolution among very closely related species was limited. Our results suggest that PPR genes can be readily employed in non-model organisms. They may be best used to resolve relationships in a spectrum from among distantly related genera to among not-so-closely related congeneric species, but may have limited use among very closely related species.

Original languageEnglish
Pages (from-to)23-35
Number of pages13
JournalMolecular Phylogenetics and Evolution
Volume54
Issue number1
DOIs
StatePublished - Jan 1 2010
Externally publishedYes

Keywords

  • Non-model organisms
  • Nuclear gene marker
  • PPR genes
  • Phylogeny
  • Verbena complex
  • Verbenaceae

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