Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

An Evaluation Of Hypervariable Plastid Amplicons As Phylogenetic Markers

Amit Dhingra¹ , Gene Peir¹ , Jeremy L. Ramdial¹ , Pamela S. Soltis² , Douglas E. Soltis³ , Kevin M. Folta¹

¹  Horticultural Sciences Department, University of Florida, Gainesville, FL 32611

²  Florida Museum of Natural History, University of Florida, Gainesville, FL 32611

³  Department of Botany, University of Florida, Gainesville, FL 32611

A recent report described a PCR-based platform for rapidly generating chloroplast sequence from a wide range of plant species. Several of the amplicons generated exhibited a high-frequency of fragment-length polymorphism across the diverse array of angiosperms we surveyed. These finite hypervariable regions were subsequently evaluated as molecular markers to examine phylogenetic relationships within lineages, including Caryophyllales and within some families of this order (e.g., Amaranthaceae). Two types of analyses were performed to validate the applicability of this approach. First, the amplicons were generated and sequenced from a range of 27 eudicots to examine the limits of the method across a large set of species. A second approach analyzed the sequences generated from closely-related species, namely a suite of representatives of Caryophyllales and a number of strawberry (Fragaria) species. The results indicate that these primer pairs represent a rapid means to generate highly variable sequences from closely related species, and that at least a subset of them may serve as useful markers in phylogenetic and/or molecular evolution analyses.