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Systematics Section / ASPT

Padolina, Joanna [1], Timme, Ruth [1], Linder, Randal [1], Briggs, Willard [2], Xu, Weijia [2], Liu, Wenguo [2], Miranker, Daniel [2].

Identification of broadly applicable nuclear DNA regions for phylogenetic reconstruction in angiosperms.

Molecular phylogenetic analyses in plants rely heavily on data from a relatively limited set of DNA regions. For many groups, these regions work well, but in some instances they are not ideal or are inappropriate. In addition, well-supported identification of the parents of hybrid species, which are particularly common in plants, will usually require multiple markers from both parents. For these reasons, we have conducted a comprehensive search for nuclear markers that will be broadly applicable to phylogenetic reconstruction in angiosperms.
We searched for putative PCR primers using MoBIoS, a database management system designed specifically for sequence data. First, we compared the complete Arabidopsis thaliana and Oryza sativa (rice) genomes and searched for all perfectly conserved DNA oligomers of at least 18 bp. Then, we filtered out low-complexity primers, such as microsatellites. From this set of sequences, we identified all of the unique primer pairs that were separated by 400 to 3000 bp in both species, yielding 13,418 combinations. We further categorized these putative pairs, and BLASTed and their intervening sequences against all GenBank plant sequences to choose primers for laboratory screening.
Candidate primer pairs were tested in PCR reactions using DNA from six Phalaenopsis (Orchidaceae) species, six Helianthus (Asteraceae) species, and six other taxa distributed throughout the angiosperms. Primer pairs were considered high quality if they amplified a single copy in the majority of species. Single copy amplifications were directly sequenced to test their level of variation. Our final result will be an interactive database, which can be used and added to by other researchers. It will be valuable to systematists looking for nuclear markers at a variety of taxonomic levels, for clarifying instances of lineage sorting, and for studying reticulate evolution.

1 - University of Texas at Austin, Section of Integrative Biology, 1 Universiy Station, #A6700, Austin, Texas, 78712, USA
2 - University of Texas at Austin, Department of Computer Sciences, 1 University Station, #C0500, Austin, Texas, 78712, USA

universal primers
molecular markers

Presentation Type: Paper
Session: 58-7
Location: Cottonwood B (Snowbird Center)
Date: Wednesday, August 4th, 2004
Time: 3:00 PM
Abstract ID:115

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