Author: Carmel Maher
Maher, Carmel, 2024 Transcript annotation and seasonal gene expression in kidney tissue of the Australian pygmy bluetongue lizard, Tiliqua adelaidensis, Flinders University, College of Science and Engineering
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Climate change is a key threatening process for endangered species world-wide. It is impacting habitat quality and potentially causing range shifts in many species as environmental conditions continue to change. The importance of assessing the genetic health of a population alongside ecological measures has been at the forefront of genetic studies in non-model organisms. Alongside other genetic measures of population diversity or measures of selection and local adaptation, RNA-seq can provide insights into which functional genes are present and being transcribed. Evidence for differential gene expression under certain conditions can also indicate how equipped an individual is to adapt to changing conditions in the shorter term and identify genes likely to be important in surviving such environmental stressors or those that may play a role in increased plasticity. Understanding what genomic regions may be involved in withstanding climate change may offer clues about a species’ survival, either in situ or when moving animals to new environments as part of assisted dispersal or translocation efforts.
The Australian pygmy bluetongue lizard, Tiliqua adelaidensis, an endangered species endemic to South Australia, has an extremely low capacity for dispersal and exists in a highly fragmented habitat resulting from human modification of the landscape through development and cropping. Climate projections for South Australia include increasing aridity, higher-than-average maximum temperatures and lower rainfall, and the suitable range for this species has been projected to shift south under increasing impacts of climate change. Long-term conservation of the species in a warming and drying climate will ultimately rely on translocation efforts and the species’ own ability to rapidly adapt to changing conditions.
The primary aim of this thesis was to identify and analyse genes that may play a role in these lizards surviving hotter, drier summers in the short term, and in the species’ ability to survive future climate change by withstanding changes to its physical environment, such as low water availability and increased temperatures. Chapter 3 outlines two methods used to generate a transcript set: assembly of de novo transcripts; and processing of full-length long-read RNA-seq data. The de novo short-read assemblies generated a larger number of transcripts and scored higher on a measure of completeness, particularly in samples with more sequenced reads. However, the long-read transcripts expressed in the kidney tissue of T. adelaidensis provided full-length transcripts that could be used to annotate putative genes and conduct gene ontology analyses. These annotated transcripts provide a reference for functional genes in this species and can be applied in future genomic research with a focus on renal function and drought resistance. A number of functional genes were implicated in renal processes and may determine how the species maintains water homeostasis in an arid climate; these were thus tested for differential gene expression.
The null hypothesis under test in Chapter 4 was that there would be no change in gene expression between groups of pygmy bluetongue individuals collected in different seasons and subject to different environmental factors. Kidney tissue samples were chosen as a focus for this study because of the involvement of kidneys in processes such as water retention. This makes them crucial organs considering our interest in genes associated with surviving the dry season. Gene expression was measured using RNA-seq technologies for eight individuals; four collected in September at the beginning of the Austral spring (the end of the Kaurna season Kudlila, the wet season) and four in late March/early April at the beginning of the Austral autumn (the end of the Kaurna season Warltati, the hot and dry season). Genes shown to be under differential expression included those for solute carriers, protein transporters, other protein binding and DNA or RNA transcription and repair factors, and a number of other receptors. These data will provide a much-needed reference for identifying and targeting other important adaptive genes expressed in the kidney of T. adelaidensis for future projects and will support concurrent studies into translocation viability and environmental response in pygmy bluetongues.
Keywords: pygmy bluetongue, gene expression, RNA-seq, Iso-seq, lizards, transcriptomics
Subject: Biological Sciences thesis
Thesis type: Doctor of Philosophy
Completed: 2024
School: College of Science and Engineering
Supervisor: Mike Gardner