Conservation and evolution of mid-west Western Australian Acacia species using whole-chloroplast DNA sequencing

Anna Victoria Williams

    Research output: ThesisDoctoral Thesis

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    Abstract

    The mid-west of Western Australia is a hotspot for plant species biodiversity, with many rare or short range endemic species. It is also heavily impacted by mining activities, which combined make conservation a priority. This thesis aims to assess the potential of high-throughput sequencing of chloroplast genomes to underpin the conservation genetics of the highly diverse and speciose genus Acacia (Fabaceae).

    This thesis focuses firstly on establishing a fully sequenced chloroplast genome for the Acacia genus, which also represents the first fully sequenced chloroplast genome of the Mimosoideae subfamily. The genome was compared to previously sequenced Fabaceae chloroplast genomes, all of which occur in the Papilionoideae subfamily and display significant rearrangements relative to Acacia. The key finding of these comparisons was the highly divergent nature of the A. ligulata clpP1 gene, which is extremely unusual in such a highly conserved gene.

    Using the A. ligulata genome as a reference, chloroplast genomes from an additional 64 Acacia species were sequenced and assembled. These genomes were used in a phylogenetic analysis of the genus, and the integration of these genome sequences with previously sequenced small amplicon sequences from throughout the Acacia genus was investigated. The results of this study suggested that the integration of these vastly different sized sequence types has the ability to significantly improve poorly supported phylogenies, particularly when utilising a whole chloroplast genome phylogeny as a constraint upon the shorter sequences.

    Further investigation of the Acacia clpP1 gene was performed using the full complement of Acacia chloroplast genome sequences. This study found that divergence in the gene was present throughout the genus with four clades in particular exhibiting extreme divergence, indicated by mutations in the ClpP1 catalytic site. Additionally, two clpP1 pseudogenes (one plastid and one nuclear) were identified in two different Acacia clades. Sequencing of the A. ligulata transcriptome ruled out the possibility of a functional nuclear clpP1 gene in this species, suggesting that despite its unusual sequence, the divergent plastid clpP1 gene is likely to be functional.

    Finally, this thesis tested whether the whole chloroplast genome was better able to distinguish between species than traditional DNA barcoding loci. The results of this study indicated that the whole chloroplast genome provided a better means of sequence based identification than the matK and rbcL barcodes, with 19 out of 26 currently recognised taxa distinguished using the chloroplast genome sequences compared to 14 and 8 taxa distinguished using matK and rbcL, respectively.

    This thesis has significantly increased our knowledge of Acacia chloroplast genome structure and content, provides a reference for further chloroplast genetics research in the Acacia genus, solidifies the backbone of the Acacia phylogeny, and takes a first step towards whole chloroplast genome DNA barcoding in Acacia, all of which informs our conservation of Acacia species.

    Original languageEnglish
    QualificationDoctor of Philosophy
    Publication statusUnpublished - 2015

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