Document ID: chunk:federal_register_of_legislation:F2022L00555:body:0:p69
Version: federal_register_of_legislation:F2022L00555
Segment Type: other
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Character Range: 215792–220524

representation sequencing – 2 methods ddRAD (3,060 SNPs in Koalas; Kjeldsen et al. 2016) or DARTseq (4,606 SNPs; Kjeldsen et al. 2019)*  Produces thousands of single-nucleotide polymorphisms (SNPs) representing genome-wide diversity                             ddRAD and DARTseq methods are not comparable; method needs to be consistent across studies to be comparable
                                                                                                                                                 Relatively cheap and reproducible (~$60 per sample; 2021)                                                                   SNPs must be called against the reference genome for the data to be comparable to future datasets
                                                                                                                                                                                                                                                                             Digestion enzymes used are predisposed to neutral regions of the genome, so data is biased towards neutral data
Target capture – current analysis 1,209 genes (Silver et al. under review)                                                                       Developed from the reference genome for any specific gene family of interest                                                Labour intensive and expensive (~$500 per sample; 2021)
                                                                                                                                                 Provides detailed information about functional genes of interest                                                            Only provides data on genes of interest
                                                                                                                                                 Can be aligned with other datasets to determine gene associations e.g. disease resistance
Exon capture – current analysis 1,163 genes (M. Lott, unpublished data)                                                                          Developed for phylogenetic analyses between different marsupial species                                                     Labour intensive and expensive
                                                                                                                                                 Can inform historical changes over time                                                                                     Only provides data on conserved gene regions
Whole genome sequencing                                                                                                                          Provide both neutral and functional diversity information across the genome                                                 Expensive (~$1,200 per sample; 2021 for 30X depth)
                                                                                                                                                 Can be aligned with other datasets to determine gene associations e.g. disease resistance, heat tolerance, taste receptors  Sequencing depth influences data quality, 7–10X depth is the same coverage as reduced representation sequencing; 30X depth provides ability to determine functional gene differences across the genome

* ddRAD = double digest restriction-site associated sequencing, digestion enzymes produce fragments approximately 120bp long; DARTseq = method developed by Diversity Arrays Technology (Canberra), digestion enzymes produce fragments approximately 75bp long
Note: scats yield low quality DNA, so scat analysis requires the use of microsatellite markers or reduced representation sequencing, although the number of SNPs obtained from scat is less than for tissue/blood samples. Target capture, exon capture and whole genome sequencing methods all require high quality DNA from either tissue or blood samples.

Using these different genetic methods, at the scale of the entire geographic population, the Koala is considered relatively genetically diverse, indicative of a healthy outbred species (Houlden et al. 1996; Johnson et al. 2018; Kjeldsen et al. 2016, 2019; Lee et al. 2010a), although genetic diversity varies at the population level (Lee et al. 2010a; Wedrowicz et al. 2018; Kjeldsen et al. 2019). Southern populations of Victoria and South Australia generally show lower genetic diversity, consistent with bottlenecks and founder events from translocations (Houlden et al. 1996; Johnson et al. 2018; Kjeldsen et al. 2019; Wedrowicz et al. 2018). South Gippsland may be an exception and is thought to be a remnant population (Wedrowicz