TY - JOUR
T1 - An empirical demonstration of using pentatricopeptide repeat (PPR) genes as plant phylogenetic tools
T2 - Phylogeny of Verbenaceae and the Verbena complex
AU - Yuan, Yao Wu
AU - Liu, Chang
AU - Marx, Hannah E.
AU - Olmstead, Richard G.
PY - 2010/1
Y1 - 2010/1
N2 - 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.
AB - 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.
KW - Non-model organisms
KW - Nuclear gene marker
KW - PPR genes
KW - Phylogeny
KW - Verbena complex
KW - Verbenaceae
UR - http://www.scopus.com/inward/record.url?scp=70649087039&partnerID=8YFLogxK
U2 - 10.1016/j.ympev.2009.08.029
DO - 10.1016/j.ympev.2009.08.029
M3 - Article
C2 - 19733248
AN - SCOPUS:70649087039
SN - 1055-7903
VL - 54
SP - 23
EP - 35
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
IS - 1
ER -