Insights from the land down under

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One of the things that immediately comes to mind when I think about Australia – besides kangaroos, dingoes, wombats, the great barrier reef, the Sydney opera house and Men at Work’s famous tune “Down Under” – is of course the cuddly and iconic koala.

These creatures are special in many ways. Not only are they the last living representative of the Phascolarctidae family, but they are also biologically unique as selective eaters of toxic eucalyptus leaves. In recent years, we have seen that koalas are struggling (1, 2), partly due to habitat loss from urbanization, climate changes, droughts and bush fires. Low genetic diversity and infections like chlamydial disease (3–6) and koala retrovirus (3, 7–11) are also taking a toll on the population (1, 2).

In 2012, research from the Australian Koala Foundation (AKF) indicated that extinctions of local koala populations have already occurred, making the koala an endangered species. In contrast to the millions of koalas that were thought to be present at the time of European settlement, the AKF stated there could be as few as only 43,000 koalas remaining. Other estimates are in the range of 144,000 – 605,000, but still show a tendency of decline (2, 12). This decline was one of the key drivers for setting up the Koala Genome Consortium in 2013. A group of Australian scientists led by Dr. Rebecca Johnson of the Australian Museum have been sharing their current knowledge and ideas about koala populations, genetics and diseases with the aim of ensuring the long-term survival of this important marsupial. To date, the consortium comprises 54 scientists from 29 institutions across seven countries and has succeeded in achieving some groundbreaking research (1).

In this recently published article (13) in Nature Genetics, Dr. Rebecca Johnson and colleagues describe their success in unlocking the koala genome through their sequencing of more than 3.4 billion base pairs and over 26,000 genes (14).

For this work, high molecular weight (HMW) DNA was extracted from heart and kidney tissue using the DNeasy Blood and Tissue Kit with RNase A treatment or from spleen tissue using Genomic-Tip 100/G columns, the DNA Buffer SetDNA Buffer Set and RNase A, followed by PacBio sequencing.

For their RNA-seq analysis of koala conjunctival tissue samples, the samples were placed directly into RNAlater Stabilization Reagent upon harvesting and stored overnight at 4°C before storing at –80°C for later analysis. For RNA extraction, the RNeasy Mini Kit was used with an on-column DNase treatment to eliminate contaminating DNA from the samples.

The results of their experiments reveal that the koala’s ability to detoxify eucalyptus foliage could be due to expansions within the cytochrome P450 gene family. In addition, the koala’s ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. Furthermore, the team identified novel lactation proteins that protect young koalas in the pouch as well as immune genes that are important in the response to chlamydial disease (13). Hopefully, these exciting results and those of future studies will give scientists the knowledge needed to reverse the decline of these special creatures.

Check out our dedicated QIAGEN site to read about other diverse teams of scientists and the remarkable discoveries they have made through challenging expeditions to Antarctica, the unearthing of ancient mysteries and blasting of cells into space.

 

References:

  1. 1. Koala Genome Consortium Link
  2. 2. Australia Koala Foundation Link
  3. 3. Madden, D. et al. (2018) Koala immunology and infectious diseases: how much can the koala bear? Dev Comp Immunol. 82, 177–185. Link
  4. 4. Polkinghorne, A., Hanger, J., and Timms, P. (2013) Recent advances in understanding the biology, epidemiology and control of chlamydial infections in koalas. Vet. Microbiol. 165, 214–223. Link
  5. 5. Dahlhausen, K.E. et al. (2018) Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment, PeerJ., 6: e4452. Link
  6. 6. Nyari S. et al. (2017) Epidemiology of chlamydial infection and disease in a free-ranging koala (Phascolarctos cinereus) population. PLoS One, 12(12):e0190114. Link
  7. 7. Waugh, C.A. et al. (2017) Infection with koala retrovirus subgroup B (KoRV-B), but not KoRV-A, is associated with chlamydial disease in free-ranging koalas (Phascolarctos cinereus). Sci. Rep., 7(1):134. Link
  8. 8. Stoye, J.P. (2006) Koala retrovirus: a genome invasion in real time. Genome Biol. 7, 241.
  9. 9. Hobbs, M. et al. (2017) Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline. Sci. Rep. 7, 15838.
  10. 10. Kinney, M.E. and Pye, G.W. (2016). Koala retrovirus: a review. J. Zoo Wildl. Med. 47, 387–396. Link
  11. 11. Denner, J. (2016) Transspecies transmission of gammaretroviruses and the origin of the gibbon ape leukaemia virus (GaLV) and the koala retrovirus (KoRV). Viruses 8:12, 336.
  12. 12. Adams-Hosking, C. et al. (2016) Use of expert knowledge to elicit population trends for the koala (Phascolarctos cinereus). Divers. Distrib. 22, 249–262. Link
  13. 13. Johnson, R.N. et al. (2018) Adaptation and conservation insights from the koala genome. Nature Genetics. Link
  14. 14. Kyoto University. “What does the koala genome tell us about the taste of eucalyptus? New data provides insight into the marsupial’s unique feeding habits.” 10 July 2018. Link

 

 

Kjell Kirschbaum

Kjell Kirschbaum, M.Sc., is a Global Market Manager based in QIAGEN’s Venlo office, the Netherlands. He trained as a bioveterinary scientist at the University of Utrecht and has hands-on experience in nucleic acid and protein purification, cell culture, PCR and qPCR technology. Kjell joined QIAGEN in 2011 as a CRM specialist, regularly interacting with customers about their day-to-day experimental needs and offering relevant solutions. Currently, he is involved in managing global projects for sample preparation and automation technologies.

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