Many people of a certain age will remember their first awareness of the koala coming from a television commercial in the 1960's for an Australian airline ("I hate Qantas"). Thereafter, of course, zoos, like the San Diego Zoo and National Zoo in Washington, D.C., developed breeding programs for these marsupials (unrelated to bears despite their earlier moniker). Today, these animals face a variety of ecological challenges and provide a biochemical conundrum with regard to their diet, which (as most know) is almost exclusively made up of eucalyptus leaves. This is a curious food source, containing a variety of toxic compounds (perhaps to ward off insect predation) that includes elevated amounts of so-called secondary metabolites, including phenolic compounds and terpenes and being so low in available calories that the animals spend up to 22 hours a day asleep. Koalas, Phascolarctos cinereus, are the only remaining species (of 15-20 fossil relatives) of the marsupial family Phascolaerctidae, having diverged from terrestrial wombats about 350,000 years ago.
Recently, an international group of investigators*, predominantly from Australian institutes but including researchers from Europe, Asia, and the U.S., reported the results of whole genome sequencing studies of three koala individuals, in a Nature Genetics article entitled "Adaptation and conservation insights from the koala genome." The results were compared with other marsupial species: platypus, opossum, wallaby, and Tazmanian devil, as set forth in this table from the report (click on table to expand):
The koala genome consists of 16 chromosomes containing an estimated 3.42 Gigabasepairs of DNA. Genetic analysis identified a total of over 26,000 genes, comprised of 6,124 protein-coding genes in 2,118 gene families, with 1,089 of these gene families having more members than orthologous family members in human, mouse, dog, tammar wallaby, Tasmanian devil, gray short-tailed opossum, platypus, or chicken. Like most eukaryotic genomes, the koala genome contains a variety of repeated sequences, with interspersed repeats making up 47.5% of the koala genome (and 44% of these repeats comprising transposable elements). Short interspersed repeats (SINEs) comprise 35.2% and long interspersed repeats (LINEs) comprise 28.9% of these repetitive elements. The study also identified non-coding RNA species and in particular a species termed RSX, which is involved in X chromosome inactivation in females (and is expressed exclusively in female tissues). Also of interest were the centromere structure of koala chromosomes, which are smaller in marsupials than eutherian mammals and comprise 2.6 Mb of the koala haploid genome (or about 300 bp per chromosome). Like other species with small centromeres (such as gibbons) the koala centromeres comprise composite repeat elements and lack "higher order satellite arrays" found in more complex centromeres from other species.
These researchers looked at particular genes and gene families that could be expected to be involved in providing means for detoxifying compounds from eucalyptus leaves and found expansion of genes encoding cytochrome P450 monooxygenases (CYP). In particular, expansion of the CYP 2 subfamily C genes was detected in the koala genome, comprising 31 members of the family, which showed (the expected) high levels of expression in liver. Fine structure genetic mapping indicated that this expansion was the result of tandem duplication of these genes, with a mixture of "purifying" selection and episodic diversifying selection at particular CYP codons. This results, according to the authors, in higher expression levels of these detoxification enzymes along with neofunctionalization. In addition to helping to explain koala dietary choices, these results are also relevant for better therapeutic intervention in treating koala diseases. For example, CYP genes are also responsible for metabolizing non-steroidal anti-inflammatory drugs and antibiotics, which can influence dosage level choices to make treatment more effective.
The koala genome also contains an expansion (six genes instead of just one in related marsupials and none in tammar wallaby, human, mouse, dog, platypus, or chicken) of the genetic lineage for vomeronasal receptor type 1, which is involved in detecting non-volatile odorants. In contrast, the number of olfactory receptor genes in koala (1,169) is slightly lower than in gray short-tailed opossum (1,431 genes), tammar wallaby (1,660 genes, and Tasmanian devil (1,279 genes). The koala genome also has had an expansion in genes enabling it to "taste water," i.e., detect leaves having a higher moisture content. The koala genome also shows expansions (24, the highest in any marsupial and almost the highest in any mammal) of genes of the TAS2R gene family, which plays a role in detecting "bitter" tasting compounds. In addition, genes in the TS1R family, which have been "pseudogenized" in giant panda (which also has a specialized diet) are fully functional in koalas.
The study also identified genes involved in induced ovulation and koala milk production, which is important due to the peculiarities of koala development (like all marsupials, where the young complete development in a pouch and is nourished by its mother's milk). These results showed a pattern of genes and gene expression that would permit the animal to "fine tune" the composition of her milk at various stages of her young's development. The study also identified a gene, the marsupial milk 1 gene, that is analogous to eutherian genes for antimicrobial proteins.
Koala populations are subject to two infectious diseases: Chlamydia pecorum and a koala-specific retrovirus (KoRV, believed to be derived from a rodent virus). The genome analysis identified "de novo assembly of complex, highly duplicated immune gene families and comprehensive annotation of immune gene clusters" that the authors believe will provide a basis for identifying genes involved, inter alia, with immune responses to various chlamydia vaccines. The authors also report characteristic patterns of differential expression of immune response-related genes in chlamydia-infected animals. "These annotated koala immune genes will now help us to define features of protective versus pathogenic immunological responses to the disease and may be invaluable for effective vaccine design," the authors believe.
The KoRV is known to be transmitted by both germline and infectious, "horizontal" mechanisms, the reference genome reported in the article having 73 insertions of this retrovirus. The genetic loci of these insertions were not, in the authors view, involved in retroviral pathogenesis, these sites being limited to introns and 3' untranslated regions (although the researchers did not discount the possibility that transcription from the retroviral long terminal repeats through to adjacent host cell genes might play a factor).
Finally, the authors were able to assess modern koala population structure in Australia within the context of the species evolutionary history with the goal of permitting better ecological choices to be made in human efforts to improve koala population viability in the wild. These studies involved mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) comparisons between individuals from geographically divergent populations. The authors conclude:
The information generated here provides a foundation for a conservation management strategy to maintain gene flow regionally while incorporating the genetic legacy of biogeographic barriers. Furthermore, the contrast in genome-wide levels of diversity between southern and northern populations highlights the detrimental consequences of the unmonitored use of small isolated populations as founders for reestablishing and/or rescuing of populations on genome-wide levels of genetic diversity.
* Rebecca N. Johnson, Denis O'Meally, Zhiliang Chen, Graham J. Etherington, Simon Y.W. Ho, Will J. Nash, Catherine E. Grueber, Yuanyuan Cheng, Camilla M. Whittington, Siobhan Dennison, Emma Peel, Wilfried Haerty, Rachel J. O'Neill, Don Colgan, Tonia L. Russell, David E. Alquezar-Planas, Val Attenbrow, Jason G. Bragg, Parice A. Brandies, Amanda Yoon-Yee Chong, Janine E. Deakin, Federica Di Palma, Zachary Duda, Mark D. B. Eldridge, Kyle M. Ewart, Carolyn J. Hogg, Greta J. Frankham, Arthur Georges, Amber K. Gillett, Merran Govendir, Alex D. Greenwood, Takashi Hayakawa, Kristofer M. Helgen, Matthew Hobbs ,Clare E. Holleley, Thomas N. Heider, Elizabeth A. Jones, Andrew King, Danielle Madden, Jennifer A. Marshall Graves, Katrina M. Morris, Linda E. Neaves, Hardip R. Patel, Adam Polkinghorne, Marilyn B. Renfree, Charles Robin, Ryan Salinas, Kyriakos Tsangaras, Paul D. Waters, Shafagh A. Waters, Belinda Wright, Marc R. Wilkins, Peter Timms and Katherine Belov
Image of koala climbing up a tree, Great Otway National Park, Victoria, Australia by Diliff, from the Wikimedia Commons under the Creative Commons Attribution-Share Alike 3.0 Unported license.
