Abstract
Gene cloning is the first step of targeted gene replacement for functional studies, discovery of gene alleles, and gene expression among other applications. In this chapter, we will describe a cloning technique suitable for fungal species where the genomic information and sequences available are limited. This strategy involves obtaining protein sequences of the gene of interest from various organisms to identify at least two conserved regions. Degenerate primers are designed from these two conserved regions and the resulting PCR products are sequenced. The sequence of the PCR products can be analyzed using suitable databases to determine their similarity to the gene/protein of interest. In cases where the entire gene cannot be cloned directly using these primers, this initial nucleotide sequence can be used as a template for further primer design and genome walking in both directions for either the cloning of a longer fragment or even the cloning of the complete gene. Here, we describe the partial cloning of a reducing polyketide synthase gene from the fungal plant pathogen Ascochyta rabiei using this strategy.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Mizushina, Yoshiyuki, et al (2002) A plant phytoxin, solanapyrone A, is an inhibitor of DNA polymerase β and λ. J Biol Chem 277: 630–638
Cox, Russell, et al (2004) Rapid cloning and expression of a fungal polyketide synthase gene involved in squalestatin biosynthesis. Chem Commun 20:2260–2261
Fujii, Isao, et al (2005) An iterative type I polyketide synthase PKSN catalyzes synthesis of the decaketide alternapyrone with region-specific octa-methylation. Chem Biol 12:1301–1309
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Delgado, J.A., Meinhardt, S., Markell, S.G., Goswami, R.S. (2012). Gene Cloning Using Degenerate Primers and Genome Walking. In: Bolton, M., Thomma, B. (eds) Plant Fungal Pathogens. Methods in Molecular Biology, vol 835. Humana Press. https://doi.org/10.1007/978-1-61779-501-5_39
Download citation
DOI: https://doi.org/10.1007/978-1-61779-501-5_39
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-500-8
Online ISBN: 978-1-61779-501-5
eBook Packages: Springer Protocols