Arbitrarily primed PCR for comparison of meta genomes and extracting useful loci from them

Leigh Burgoyne, Lin Y. Koh, David Catcheside

    Research output: Chapter in Book/Report/Conference proceedingChapter

    3 Citations (Scopus)

    Abstract

    A method is described that uses arbitrarily primed PCR followed by many cycles of amplification under stringent conditions and selection by computational means to obtain a set of sequence tags that can be used for the comparison of metagenomes. Relative to unselective shot-gun sequencing, the results are small data sets that can be csompared electronically or plotted as scattergrams that are simple to interpret. The method can be used to compare groups of samples of any size to build in-house databases from which, for example, the provenance of trace soil samples may be inferred. The method also allows for selection of primers with locus-specificity and an example is given in which a South Australian sequence-related to a Portuguese thermophile (Rubrobacter radiotolerans) is extracted and tested on a set of soils.

    Original languageEnglish
    Title of host publicationPCR
    Subtitle of host publicationMethods and protocols
    EditorsLucília Domingues
    Place of PublicationNew York
    PublisherHumana Press Inc.
    Chapter18
    Pages267-280
    Number of pages14
    ISBN (Electronic)9781493970605
    ISBN (Print)9781493970599
    DOIs
    Publication statusPublished - 25 May 2017

    Publication series

    NameMethods in Molecular Biology
    Volume1620
    ISSN (Print)1064-3745

    Keywords

    • 50mers
    • Forensic
    • Metagenome analysis
    • PCR
    • Primer design
    • Sequence tags
    • Soils
    • Polymerase chain reaction (PCR)

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  • Cite this

    Burgoyne, L., Koh, L. Y., & Catcheside, D. (2017). Arbitrarily primed PCR for comparison of meta genomes and extracting useful loci from them. In L. Domingues (Ed.), PCR: Methods and protocols (pp. 267-280). (Methods in Molecular Biology; Vol. 1620). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7060-5_18