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A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats¹

Section of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station C0930, Austin, Texas 78712 USA; DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, California, 94598 USA; Department of Integrative Biology, University of California, 3060 Valley Life Sciences Building #3140, Berkeley, California 94720 USA; Genome Project Solutions, 1024 Promenade Street, Hercules, California 94547 USA

ABSTRACT

We have sequenced two complete chloroplast genomes in the Asteraceae, Helianthus annuus (sunflower), and Lactuca sativa (lettuce), which belong to the distantly related subfamilies, Asteroideae and Cichorioideae, respectively. The Helianthus chloroplast genome is 151 104 bp and the Lactuca genome is 152 772 bp long, which is within the usual size range for chloroplast genomes in flowering plants. When compared to tobacco, both genomes have two inversions: a large 22.8-kb inversion and a smaller 3.3-kb inversion nested within it. Pairwise sequence divergence across all genes, introns, and spacers in Helianthus and Lactuca has resulted in the discovery of new, fast-evolving DNA sequences for use in species-level phylogenetics, such as the trnY-rpoB, trnL-rpl32, and ndhC-trnV spacers. Analysis and categorization of shared repeats resulted in seven classes useful for future repeat studies: double tandem repeats, three or more tandem repeats, direct repeats dispersed in the genome, repeats found in reverse complement orientation, hairpin loops, runs of A's or T's in excess of 12 bp, and gene or tRNA similarity. Results from BLAST searches of our genomic sequence against expressed sequence tag (EST) databases for both genomes produced eight likely RNA edited sites (C U changes). These detailed analyses in Asteraceae contribute to a broader understanding of plastid evolution across flowering plants.

Key Words: Asteraceae • chloroplast DNA • comparative genomics • divergent sequence • genomic repeats • Helianthus annuus • Lactuca sativa • RNA editing

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