Biology subjects

Peel, E.

Publications and source records attributed to Peel, E..

6 recordsLinked to original sources

bioRxiv2025

Characterisation of pouch secretions from breeding Tasmanian devils

Tasmanian devils (Sarcophilus harrisii), like all marsupials, give birth to altricial young. Here we employ proteomic analysis to identify components of devil pouch secretions (red oil) that may contribute to offspring survival and development. Proteins were extracted from 5 samples and analysed by liquid chromatography-tandem mass spectrometry. Peptide-level evidence revealed proteins involved in a diverse set of immune pathways, including those mediating iron-ion transport, defence responses to bacteria, innate immune responses, and antigen processing. A core set of 200 proteins was identified across at least three samples, 63 of which were associated with antimicrobial or immunoregulatory functions. These included immunoglobulins, components of complement and coagulation cascade, and antimicrobial proteins and peptides. For the first time, these findings highlight the Tasmanian devils red oil secretions as a source of immune proteins likely contributing to microbiome restructuring during lactation. Moreover, the data indicate that these proteins may act synergistically in pathways triggered by immune challenges or physiological stress. In briefMicrobial shifts in the Tasmanian devil pouch are critical for establishing a protective environment for the developing joey. This study confirms that Tasmanian devil red oil contains a diverse array of immune proteins that likely contribute to these microbial shifts.

zoology↗

bioRxiv2025

When Cells Rebel: a comparative genomics investigation into marsupial cancer susceptibility

Cancer is ubiquitous in multicellular life, yet susceptibility varies significantly between species. Previous studies have shown a genetic basis for cancer resistance in many species, but few studies have investigated the inverse: why some species are particularly susceptible to cancer. The Dasyuridae are a family of carnivorous marsupials that are frequently reported as having high rates of cancer prevalence. We hypothesised that this high susceptibility also has a genetic basis. To investigate this, we generated reference genomes for the kowari (Dasyuroides byrnei), a dasyurid species with one of the highest rates of reported cancer prevalence among mammals, and a non-dasyurid marsupial, the eastern barred bandicoot (Perameles gunnii). We used these to perform a comparative genomics analysis alongside nine previously assembled reference genomes: four dasyurid species and five non-dasyurid marsupial species. Genomes were annotated using FGENESH++ and assigned to orthogroups for input to CAFE (Computational Analysis of gene Family Evolution) analysis to identify gene families that had undergone significant expansions or contractions in each lineage. In the dasyurids, we identified large expansions in Ras genes, a family of oncogenes. Interestingly, a similar expansion of Ras genes was also identified in the bandicoot and bilby. These genes were primarily expressed in tissues such as testes, ovaries and yolk sac, so we hypothesise they serve a reproductive role. Future work is required to identify the potential roles of oncogene expansions in cancer susceptibility in these marsupial species.

genomics↗

bioRxiv2024

Temporal loss of genome-wide and immunogenetic diversity in a near-extinct parrot

Loss of genetic diversity threatens a species adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a Critically Endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016 and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary and historical resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 {+/-} 0.000699 SD) and contemporary (0.00057 {+/-} 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples was also observed. A temporal reduction of the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 {+/-} 2.73; contemporary = 3.89 {+/-} 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridization and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred this species in order to prevent extinction. Significance statementOrange-bellied parrots (Neophema chrysogaster) face a dire future, with extinction predicted by 2038 due to severe genetic diversity loss. This Critically Endangered species, now reduced to a single wild population and a captive breeding program, has lost 62% of its genomic diversity since 1829. Contemporary samples show a decline in immunogenetic diversity and signs of very recent inbreeding. Meaning birds today are more susceptible to disease events than birds a hundred years ago. Conservation efforts must consider hybridization and synthetic biology to counteract the catastrophic loss of genetic diversity to ensure the species survival. Our study underscores the urgent need for innovative strategies to preserve the adaptive potential and resilience of the orange-bellied parrot and other species in similar situations.

genomics↗

bioRxiv2023

Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides

The number of genome-level resources for non-model species continues to rapidly expand. However, frog species remain underrepresented, with up to 90% of frog genera having no genomic or transcriptomic data. Here, we assemble the first genomic and transcriptomic resources for the recently described southern stuttering frog (Mixophyes australis). The southern stuttering frog is ground-dwelling, inhabiting naturally vegetated riverbanks in south-eastern Australia. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated a high-quality genome assembly, with a scaffold N50 of 369.3 Mb and 95.1% of the genome contained in twelve scaffolds. Using this assembly, we identified the mitochondrial genome, and assembled six tissue-specific transcriptomes. We also bioinformatically characterised novel sequences of two families of antimicrobial peptides (AMPs) in the southern stuttering frog, the cathelicidins and {beta}-defensins. While traditional peptidomic approaches to peptide discovery have typically identified one or two AMPs in a frog species from skin secretions, our bioinformatic approach discovered 12 cathelicidins and two {beta}-defensins that were expressed in a range of tissues. We investigated the novelty of the peptides and found diverse predicted activities. Our bioinformatic approach highlights the benefits of multi-omics resources in peptide discovery and contributes valuable genomic resources in an under-represented taxon.

genomics↗

bioRxiv2022

Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial

The numbat (Myrmecobius fasciatus) is a critically endangered Australian marsupial, and the last surviving member of the Myrmecobiidae family. The numbat regularly undergoes torpor and is unique amongst marsupials as it is the only diurnal and termitivorous species. Here we sequenced the first draft genome of the numbat using 10x Genomics chromium linked-read technology, resulting in a 3.42 Gbp genome with a scaffold N50 of 223 Kbp. A global transcriptome from liver, lung and tongue was also generated to aid genome annotation with Fgenesh++, identifying 21,465 protein-coding genes and 78.7% complete mammalian BUSCOs. To investigate adaptation to the numbats termitivorous diet and arid/semi-arid range, we interrogated the most highly expressed transcripts within the tongue and manually annotated taste, vomeronasal and aquaporin gene families. Antimicrobial proteins and proteins involved in digestion were highly expressed in the tongue, as expected. Similarly, umami taste receptors were also expressed in the tongue, however sweet taste receptors were not expressed in this tissue. This pattern of taste receptor expression, combined with the putative contraction of the bitter taste receptor gene repertoire in the numbat genome, may indicate a potential evolutionary adaptation to their specialized termitivorous diet. Vomeronasal and aquaporin gene repertoires were similar to other marsupials and have not undergone expansion or contraction. The draft numbat genome is a valuable tool for conservation and can be applied to population genetics/genomics studies and to investigate the unique biology of this interesting species.

genomics↗

bioRxiv2021

A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi

Biodiversity is declining globally, and Australia has one of the worst extinction records for mammals. The development of sequencing technologies means that genomic approaches are now available as important tools for wildlife conservation and management. Despite this, genome sequences are available for only 5% of threatened Australian species. Here we report the first reference genome for the woylie (Bettongia penicillata ogilbyi), a critically endangered marsupial from Western Australia, and the first genome within the Potoroidae family. The woylie reference genome was generated using Pacific Biosciences HiFi long-reads, resulting in a 3.39 Gbp assembly with a scaffold N50 of 6.49 Mbp and 86.5% complete mammalian BUSCOs. Assembly of a global transcriptome from pouch skin, tongue, heart and blood RNA-seq reads was used to guide annotation with Fgenesh++, resulting in the annotation of 24,655 genes. The woylie reference genome is a valuable resource for conservation, management and investigations into disease-induced decline of this critically endangered marsupial.

genomics↗