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Recent Topics Posters

Shaw, Joey [1], Lickey, Edgar [1], Schilling, Edward [1], Small, Randall [1].

The tortoise and the hare III: comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms.

Noncoding sequences of the chloroplast genome provide a primary source of data for interspecific phylogenetic and intraspecific phylogeographic studies. While the chloroplast genome contains hundreds of noncoding regions, relatively few of these have been exploited for phylogenetics. In a recent study from our labs (Shaw et al. 2005 Amer. J. Bot. 92:142-166) we evaluated the relative phylogenetic utility of 21 noncoding chloroplast regions using ten seed plant lineages. The results of that study showed that (1) there is predictable variation in the phylogenetic utility of different noncoding regions, and (2) the most variable noncoding regions have rarely been employed, while the most widely used regions are among the least variable. That study assessed the utility of many previously published regions and led us to conclude that unexplored, highly variable regions of the chloroplast genome may exist. To address the potential utility of additional regions we compared published whole chloroplast genome sequences from three disparate angiosperm lineages: Atropa vs. Nicotiana (Solanaceae, Asterid); Lotus vs. Medicago (Fabaceae, Rosid); Saccharum vs. Oryza (Poaceae, Monocot). For each pair of chloroplast genome sequences we aligned the entire large and small single copy regions and tabulated the number of variable sites for each noncoding region (introns and intergenic spacers). Based on the number of variable sites in these comparisons we chose 13 noncoding regions to evaluate further. PCR-amplification primers were designed for these 13 regions and used to amplify and sequence them from seven angiosperm lineages (a subset of the ten lineages used in the previous study). The results show that these new regions may offer levels of variation comparable to or better than the best regions identified in the earlier study, thus providing the plant systematics community with several additional quickly evolving noncoding chloroplast regions for phylogenetic and phylogeographic studies.


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1 - University of Tennessee, Department of Ecology and Evolutionary Biology, 437 Hesler Biology Building, 1406 Circle Drive, Knoxville, Tennessee, 37996-1100, USA

Keywords:
angiosperms
intergenic spacers
introns
Phylogeny
molecular systematics
Chloroplast DNA.

Presentation Type: Recent Topics Poster
Session: 33-128
Location: Salon C, D & E - Gov Ballroom/Hilton
Date: Tuesday, August 16th, 2005
Time: 12:30 PM
Abstract ID:629


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