A data base for PCR primers in the chloroplast genome
Heinze B.

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Introduction
Methods
The data base, and some applications
Conclusions
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A Data Base of PCR Primers for the Study of the Chloroplast Genome in Plants

Berthold Heinze

Federal Research Centre for Forests, Genetics Department, Vienna, AUSTRIA

Version 2.1 (March 2007 - more than 700 primer sequences)



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Introduction

Several authors have described the use of "universal" primers for PCR from chloroplast DNA, i.e., primers that amplify DNA fragments from many species in a genus, family, or even higher taxonomic groupings (see dedicated list of references). Usually, such primers are based on conserved DNA sequence in exons. The information is contained in a few comprehensive articles and many scattered primer sequences in other publications. For use in molecular population genetics and taxonomy, large numbers of markers are necessary. Their (known) levels of polymorphism should fit diverse applications. They should be applicable for many species, and lend temselves to rapid screening methods. However, marker development for such 'universal PCR' is time-consuming, so markers that can be transferred between species are desirable. This is possible with 'classical' RFLP probes. As shown by several authors, it is also possible with PCR primers, but to what extent ? The database compiled here will provide a starting ground to estimate primer 'universality'. In chloroplast spacers, gene order is highly conserved, and spacers show intra-species variation. Small indels predominate. Exon sequences are generally highly conserved, but this depends on the gene in question. Some problems with universal PCR include the more rapid sequence evolution in some parts of the chloroplast; the identification of polymorphisms between conserved primer sites (introns); and occasional rearrangements, deletions, duplications in some genera, families, or higher taxonomic groups. Sets of dedicated 'universal' chloroplast primers for amplifying spacers and introns have been described by Taberlet et al. 1991, Demesure et al. 1995, Dumolin-Lapegue et al. 1997, Fofana et al. 1997, Hamilton 1999, and Grivet et al. 2001. In the latter publication, the large single copy region of the chloroplast ring is covered by 38 primer pairs. Amplified fragments can be analysed by restriction or sequencing. 'Universal' chloroplast primers have also been developed for comparative sequencing in phylogeny, e.g. in the rbcL gene, for obtaining phylogenies of land plants. Other genes with different mutation rates can resolve certain problems, e.g. matK, ndhF, rpl16, and atpB.

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