Isolating microsatellite markers in the marine sponge Cinachyrella alloclada for use in community and population genetics studies

  • Sarah Griffiths

    Student thesis: Unknown


    Molecular genetics is commonly used to address ecological questions and aid in ecosystem management and conservation. The level of genetic variation, and its distribution among populations, has ecologically important consequences, such as for associated community biodiversity and ecological resilience. Microsatellites are popular and useful molecular markers with many applications, but must be developed a priori for every species, which traditionally has been a costly and time-consuming process. Recently, next-generation sequencing approaches have been successfully used to isolate microsatellite markers for a lower cost and much more quickly than traditional methods offer. Here, we develop an existing method that uses Illumina paired-end sequencing, to isolate microsatellites for the marine sponge Cinachyrella alloclada. We use longer read lengths than previously used (2 x 250bp) and filter sequence data by quality in order to increase the number of amplifiable loci located and the chances of successful amplification. Out of 35 loci tested, 13 were successfully amplified in PCR reactions. These loci can go on to be used in population genetics and community genetics studies for C. alloclada, aiding understanding of its ecology. In addition, this method of microsatellite isolation offers a faster and cheaper way of obtaining molecular markers than traditional approaches, and uses quality filtering and longer read lengths to enhance the capture of amplifiable loci. This method may therefore be used for other species that would benefit from the availability of microsatellite markers, including other understudied marine sponges.
    Date of Award31 Dec 2014
    Original languageEnglish
    Awarding Institution
    • The University of Manchester
    SupervisorRichard Preziosi (Supervisor)


    • microsatellite
    • population genetics

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