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Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing
Reinhold Stockenhuber1, Stefan Zoller2, Rie Shimizu-Inatsugi3
1Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland; Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
Plos One
|June 11, 2015
Summary
Researchers developed a cost-effective method using next-generation sequencing (NGS) to create thousands of nuclear primer pairs for the Brassicaceae family. These primers are broadly applicable for genetic studies in diverse mustard species.
Area of Science:
- Genomics and Bioinformatics
- Molecular Evolution
- Plant Science
Background:
- Limited DNA sequence data for non-model organisms hinders the development of universally applicable primers for nuclear marker studies.
- Next-generation sequencing (NGS) offers a powerful solution to overcome this data limitation in molecular ecology and evolution.
Purpose of the Study:
- To develop a flexible, inexpensive method for identifying numerous nuclear primer pairs applicable across most Brassicaceae species.
- To create a valuable genomic resource for addressing new questions in Brassicaceae evolutionary and population genetics.
Main Methods:
- Mapped NGS transcriptome reads from Cardamine hirsuta and Arabis alpina to the Arabidopsis thaliana reference genome.
- Bioinformatically identified conserved sequence motifs to design primer pairs for nuclear protein coding loci (NPCL) and exon-primed intron-crossing (EPIC) sequences.
- Validated primer pair universality and amplicon specificity across 30 Brassicaceae taxa.
Main Results:
- Identified 2,334 universally applicable primer pairs targeting 1,164 genes, providing a substantial resource for Brassicaceae research.
- A majority of tested primer pairs yielded single amplicons in all investigated Brassicaceae taxa, demonstrating high specificity.
- Phylogenetic analyses using a subset of markers confirmed their utility across varying phylogenetic divergences within the family.
Conclusions:
- The developed method is a cost-effective approach for designing nuclear loci applicable to a broad range of Brassicaceae taxa.
- The identified primer pairs are a readily usable genomic resource, facilitating phylogenetic and population genetic studies in the mustard family.
- This approach is compatible with current NGS technologies, enabling broader genomic research in understudied plant families.
