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.

Comments

©2007 Nature Publishing Group

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015

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