Selecting Nuclear Sequences for Fine Detail Molecular Phylogenetic Studies in Plants: A Computational Approach and Sequence Repository

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Abstract:

Abstract—

When studying the phylogenetic relationships of closely related species, it is often difficult to find nuclear DNA regions that are both easy to amplify across taxa and contain informative characters. To address this problem, we have created a database of gene sequences specifically selected to greatly increase both the likelihood of amplification across the species of interest and the likelihood of retrieving nuclear regions that are variable among these species. This result is achieved by designing primers flanking putative intron splicing sites within highly conserved genes. Over 40 species were sampled spanning rosids (14 taxa), asterids (12 taxa), grasses (seven taxa) and other angiosperms, as well as several gymnosperms, a moss, and a green alga.

Keywords: Low copy nuclear genes; database; introns

Document Type: Research Article

DOI: http://dx.doi.org/10.1600/036364412X616576

Publication date: January 1, 2012

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