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Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation
Jeanne Tonnabel1, Isabelle Olivieri, Agnès Mignot
1Université Montpellier 2, CNRS, Institut des Sciences de l'Évolution (UMR 5554), Place Eugène Bataillon, 34095 Montpellier cedex 05, France.
Molecular Phylogenetics and Evolution
|August 17, 2013
Summary
Developing new nuclear markers aids species phylogeny reconstruction for non-model organisms. This method, using transcriptomic data, successfully identified seven markers, improving phylogenetic resolution for the genus Leucadendron.
Area of Science:
- * Molecular Phylogenetics
- * Genomics
- * Bioinformatics
Background:
- * Reconstructing species-level phylogenies for non-model groups is challenging due to limited molecular data and low polymorphism.
- * Low-copy nuclear exons and non-coding regions, like 3' untranslated regions (3'-UTRs), offer valuable nuclear DNA variation.
- * Traditional markers like the ribosomal internal transcribed spacer region (ITS) may not always provide sufficient resolution.
Purpose of the Study:
- * To present a novel methodology for identifying new nuclear orthologous markers from public databases and transcriptomic data.
- * To develop and validate PCR primers for non-model organisms, specifically the genus Leucadendron (Proteaceae).
- * To assess the phylogenetic utility of newly identified markers compared to the ITS region.
Main Methods:
- * Utilized public nucleotide databases and next-generation sequencing-generated transcriptomic data to identify nuclear orthologous markers.
- * Designed PCR primers with a framework to minimize paralogy and maximize polymorphism, anchoring primers in coding regions and 3'-UTRs.
- * Sequenced and analyzed seven new nuclear markers, including three with 3'-UTRs, and compared their phylogenetic potential with the ITS region.
Main Results:
- * Successfully identified seven new nuclear markers, three of which incorporate 3'-UTRs, for the genus Leucadendron.
- * Sequenced 3'-UTRs exhibited higher polymorphism rates than the ITS region.
- * The new markers significantly improved the phylogeny of the genus Leucadendron without major incongruences with the ITS signal.
Conclusions:
- * The presented methodology is efficient for isolating orthologous nuclear loci in non-model groups.
- * This approach is broadly applicable to any non-model group with available transcriptomic data.
- * The newly developed markers, particularly those including 3'-UTRs, enhance phylogenetic resolution and are valuable for evolutionary studies.
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