Journal
MOLECULAR ECOLOGY RESOURCES
Volume 8, Issue 6, Pages 1344-1347Publisher
WILEY
DOI: 10.1111/j.1755-0998.2008.02229.x
Keywords
group II introns; internal primers; noncoding chloroplast DNA; secondary structure; sequence comparison
Funding
- NSF [DEB-0515828, ARC-0508101]
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Chloroplast group II introns offer high-quality, rapidly evolving single-copy loci for comparative sequence analysis. These introns feature diagnostic secondary structures with loops that are among the least evolutionarily constrained sequence in plastomes. We exploited these structures to develop universal primers that amplify and sequence the large Domain IV (D4) loop in several angiosperm introns. With a single sequence read, we recover 300-600 nucleotides of highly variable sequence across angiosperms, with rates of change that are equal to or higher than many of the best known intergenic spacers in plant chloroplast genomes.
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