Biology Faculty Articles
Title
Designing and Optimizing Comparative Anchor Primers for Comparative Gene Mapping and Phylogenetic Inference
Document Type
Article
Publication Date
11-2007
Publication Title
Nature Protocols
ISSN
1754-2189
Volume
2
Issue/No.
11
First Page
3022
Last Page
3030
Abstract
Here we describe protocols for designing, optimizing and implementing conserved anchor primers for use in genome mapping or phylogenetic applications, with particular emphasis on homologous gene sequences among mammals. The increasing number of whole genome sequences in public databases makes this approach applicable across a wide range of taxa. Genome sequences from representatives of two or more divergent subclades within a taxonomic group of interest are used to identify candidate local alignments (i.e., exons, exons spanning introns or conserved 5'- or 3'-untranslated regions) that contain sequences with appropriate variability for the chosen downstream application. PCR primers are designed to maximize amplification success across a broad range of taxa, and are optimized under a touchdown thermocycling protocol. Based on the initial optimization results, primers are selected for application in a diverse sampling of species, or for mapping the genome of a target species of interest. We discuss factors that have to be considered for experimental design of broad-scope phylogenetic studies. With this protocol, primers can be designed, optimized and implemented within as little as 1-2 weeks.
NSUWorks Citation
Murphy, William J. and Stephen J. O'Brien. 2007. "Designing and Optimizing Comparative Anchor Primers for Comparative Gene Mapping and Phylogenetic Inference." Nature Protocols 2, (11): 3022-3030. https://nsuworks.nova.edu/cnso_bio_facarticles/489
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
Comments
©2007 Nature Publishing Group