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Making the first step: practical considerations for the isolation of low-copy nuclear sequence markers

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Abstract:

In many plant groups, the use of low-copy nuclear sequence markers for phylogenetics and population genetics has been hindered by their limited availability. Although it may be possible to PCR amplify low-copy markers using primers designed for use with other plant groups, this does not always yield the desired results. Here, we suggest several alternative approaches to begin the isolation and characterisation of novel low-copy markers when there is little or no sequence information available. These alternatives are: (1) the design of new primers from information in the sequence databases; (2) isolation of homologous DNA using a gene probe from another organism; (3) characterisation of sequence markers from DNA fingerprints; and (4) obtaining novel sequences via cDNA cloning.

Keywords: LOW-COPY DNA SEQUENCES; MOLECULAR PHYLOGENETICS; NUCLEAR MARKERS

Document Type: Research Article

Affiliations: 1: Department of Systematic and Evolutionary Botany, Institute of Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria 2: Department of Evolutionary Biology, Institute of Zoology, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria

Publication date: 2005-08-01

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