The pentatricopeptide repeat (PPR) gene family, a tremendous resource for plant phylogenetic studies

Despite the paramount importance of nuclear gene data in plant phylogenetics, the search for candidate loci is believed to be challenging and time-consuming. Here we report that the pentatricopeptide repeat (PPR) gene family, containing hundreds of members in plant genomes, holds tremendous potential as nuclear gene markers. We compiled a list of 127 PPR loci that are all intronless and have a single orthologue in both rice (Oryza sativa) and Arabidopsis thaliana. The uncorrected p-distances were calculated for these loci between two Arabidopsis species and among three Poaceae genera. We also selected 13 loci to evaluate their phylogenetic utility in resolving relationships among six Poaceae genera and nine diploid Oryza species. PPR genes have a rapid rate of evolution and can be best used at intergeneric and interspecific levels. Although with substantial amounts of missing data, almost all individual data sets from the 13 loci generate well-resolved gene trees. With the unique combination of three characteristics (having a large number of loci with established orthology assessment, being intronless, and being rapidly evolving), the PPR genes have many advantages as phylogenetic markers (e.g. straightforward alignment, minimal effort in generating sequence data, and versatile utilities). We perceive that these loci will play an important role in plant phylogenetics. New Phytologist (2009) 182: 272-283doi: 10.1111/j.1469-8137.2008.02739.x.