University of Canterbury Home
    • Admin
    UC Research Repository
    UC Library
    JavaScript is disabled for your browser. Some features of this site may not work without it.
    View Item 
    1. UC Home
    2. Library
    3. UC Research Repository
    4. Faculty of Science | Te Kaupeka Pūtaiao
    5. Science: Theses and Dissertations
    6. View Item
    1. UC Home
    2.  > 
    3. Library
    4.  > 
    5. UC Research Repository
    6.  > 
    7. Faculty of Science | Te Kaupeka Pūtaiao
    8.  > 
    9. Science: Theses and Dissertations
    10.  > 
    11. View Item

    Conservation and Evolution of Microsatellites in Vertebrate Genomes (2008)

    Thumbnail
    View/Open
    thesis_fulltext.pdf (5.983Mb)
    Type of Content
    Theses / Dissertations
    UC Permalink
    http://hdl.handle.net/10092/1595
    http://dx.doi.org/10.26021/8100
    
    Thesis Discipline
    Biological Sciences
    Degree Name
    Doctor of Philosophy
    Publisher
    University of Canterbury. Biological Sciences
    Collections
    • Science: Theses and Dissertations [4774]
    Authors
    Buschiazzo, Emmanuel
    show all
    Abstract

    Microsatellites are strings of short DNA motifs (≤6 bp) repeated in tandem across genomes of both prokaryotes and eukaryotes. In 20 years, they became popular genetic markers, successfully employed in the field of genetic mapping and gene hunting, as well as to address various biological questions at the individual, family, population and species level. However, evolutionary and demographic inferences from microsatellite polymorphism are hampered by controversy and ambiguity in the mutational processes of microsatellite sequences. Drawing on new data from genome projects, I review in Chapter 1 the concept of a microsatellite life cycle, which hypothesizes that microsatellites follow a life cycle from birth, through expansion, contraction, death and potentially resurrection. To document and understand this integrative concept of evolution, which could help improve current models of microsatellite evolution, there is an implicit need to study the evolution of microsatellites above the species level. A prerequisite of such comparative studies is therefore to find microsatellite loci that are conserved between different species. The near or full completion of many vertebrate genomes and their alignment against one another offer the ultimate approach to find genomic elements conserved over a large evolutionary scale. In Chapter 2, I present a new comprehensive method to find conserved microsatellites in whole genomes. Using the multiple-alignment of the human genome against those of 11 mammalian and five non-mammalian vertebrates, I examine the genomewide conservation of microsatellites, and challenge the general assumption that microsatellites are too labile to be maintained in distant species. In Chapter 3, I present similar results using the alignment of the newly sequenced platypus genome against those of three mammals, the chicken and the lizard, and incorporate these data into the framework created by the 17-genome analysis. This enlarged dataset was ground for attempting to reconstruct a vertebrate phylogeny from the presence/absence of microsatellites in the different genomes. Maximum parsimony analyses resulted in a tree much similar to that of the current view of the vertebrate phylogeny, while Bayesian analyses showed some discrepancies. This work opens a way for novel theoretical developments regarding the inference of ancestral states of microsatellites. In Chapter 4, I show how knowledge on conserved microsatellite sites can help for the development of a set of comparative primers useful across the Mammalia; implementing a similar protocol, nine conserved dinucleotide repeats were genotyped in 20 unrelated individuals of 18 species (nine sister species) encompassing the mammalian phylogeny, including marsupials and monotremes, and four microsatellites were sequenced in 4 individuals per species. My results emphasize conserved microsatellites as a new resource for genetic mapping and population studies. Finally, in Chapter 5, I recount the unexpected extent of structural change among mammalian orthologous microsatellites, including change of complexity, motif replacement and overall length variability. Altogether, these findings provide a comprehensive framework that may help in many areas of research, including molecular ecology, genome mapping, population genetics, and genome and microsatellite evolution.

    Keywords
    comparative genomics; simple sequence repeats (SSRs); genome evolution; mammals; cross-species primers
    Rights
    Copyright Emmanuel Buschiazzo
    https://canterbury.libguides.com/rights/theses

    Related items

    Showing items related by title, author, creator and subject.

    • Comparative genomics of microsatellite abundance: a critical analysis of methods and definitions 

      Jentzsch, Iris Miriam Vargas (University of Canterbury. Biological Sciences, 2009)
      This PhD dissertation is focused on short tandemly repeated nucleotide patterns which occur extremely often across DNA sequences, called microsatellites. The main characteristic of microsatellites, and probably the reason ...
    • Microsatellite Evolution in The Yeast Genome - A Genomic Approach 

      Merkel, Angelika (University of Canterbury. School of Biological Sciences, 2008)
      Microsatellites are short (1-6bp long) highly polymorphic tandem repeats, found in all genomes analyzed so far. Popular genetic markers for many applications including population genetics, pedigree analysis, genetic mapping ...
    • An Investigation of Links Between Simple Sequences and Meiotic Recombination Hotspots 

      Bagshaw, Andrew Tobias Matthew (University of Canterbury. Biological Sciences, 2008)
      Previous evidence has shown that the simple sequences microsatellites and poly-purine/poly-pyrimidine tracts (PPTs) could be both a cause, and an effect, of meiotic recombination. The causal link between simple sequences ...
    Advanced Search

    Browse

    All of the RepositoryCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThesis DisciplineThis CollectionBy Issue DateAuthorsTitlesSubjectsThesis Discipline

    Statistics

    View Usage Statistics
    • SUBMISSIONS
    • Research Outputs
    • UC Theses
    • CONTACTS
    • Send Feedback
    • +64 3 369 3853
    • ucresearchrepository@canterbury.ac.nz
    • ABOUT
    • UC Research Repository Guide
    • Copyright and Disclaimer
    • SUBMISSIONS
    • Research Outputs
    • UC Theses
    • CONTACTS
    • Send Feedback
    • +64 3 369 3853
    • ucresearchrepository@canterbury.ac.nz
    • ABOUT
    • UC Research Repository Guide
    • Copyright and Disclaimer