Publications

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

Posted on by

Type: Journal Article

Reference: Tang, S., Peel, E., Belov, K., Hogg, C. J., & Farquharson, K. A. (2024). Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides. Scientific Reports, 14(1), 3991. https://doi.org/10.1038/s41598-024-54522-x

Abstract

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 β-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 β-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.

Remnant kenngoor (Phascogale calura) retain genetic connectivity and genetic diversity in a highly fragmented landscape

Posted on by

Type: Journal Article

Reference: de Visser, R. S., Hall, M., Ottewell, K., Pierson, J. C., Sanders, A., Friend, J. A., Berry, L., Hogg, C. & Catullo, R. A. (2024). Remnant kenngoor (Phascogale calura) retain genetic connectivity and genetic diversity in a highly fragmented landscape. Conservation Genetics, 1-15. https://doi.org/10.1007/s10592-024-01603-z

Abstract

Kenngoor (Phascogale calura) persist in < 1% of their original distribution, occupying highly fragmented remnant habitat in south-west Western Australia, with very little known of the genetic diversity of the remaining wild populations. Recently, the species has been translocated to managed reserves to improve its conservation. Understanding genetic structure and patterns of genetic diversity is crucial to inform conservation translocations for species recovery. This study aims to (1) assess genetic structure and genetic diversity across remaining wild locations, (2) assess long-term genetic outcomes of a mixed-source wild-to-wild translocation, and (3) estimate global effective population size. We genotyped 209 samples from 13 locations of fragmented remnant habitat using reduced representation sequencing. An isolation by distance model best explained genetic structure across the survey areas, with evidence of fine scale divergence of two northern locations. Allelic richness and autosomal heterozygosity measures indicated that diversity is spread uniformly across locations, and no locations showed signs of inbreeding or strong genetic drift. The mixed-source translocation has retained the diversity of the wider species ten years post-translocation. Overall, our results suggest that connectivity between survey areas has largely been maintained and that no location has substantially lower genetic diversity, despite the highly fragmented nature of remnant kenngoor habitat. Future translocations should aim to represent a mixture of genetically divergent locations to maintain the diversity present at the species level. Ongoing conservation management will be required to ensure the long-term viability of the species in this fragmented landscape.

Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates

Posted on by

Type: Journal article

Reference: Toby G L Kovacs, James Walker, Simon Hellemans, Thomas Bourguignon, Nikolai J Tatarnic, Jane M McRae, Simon Y W Ho, Nathan Lo, Dating in the Dark: Elevated Substitution Rates in Cave Cockroaches (Blattodea: Nocticolidae) Have Negative Impacts on Molecular Date Estimates, Systematic Biology, Volume 73, Issue 3, May 2024, Pages 532–545, https://doi.org/10.1093/sysbio/syae002

Abstract

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analyzed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by phylogenetic analyses of mitochondrial genomes and UCE loci. Furthermore, Bayesian dating analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all 13 major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.

A chromosome-level genome assembly for the dugong

Posted on by

Type: Journal Article

Reference: Dorothy Nevé Baker, Linelle Abueg, Merly Escalona, Katherine A Farquharson, Janet M Lanyon, Diana Le Duc, Torsten Schöneberg, Dominic Absolon, Ying Sims, Olivier Fedrigo, Erich D Jarvis, Katherine Belov, Carolyn J Hogg, Beth Shapiro, A chromosome-level genome assembly for the dugong (Dugong dugon), Journal of Heredity, Volume 115, Issue 2, March 2024, Pages 212–220, https://doi.org/10.1093/jhered/esae003

Abstract

The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and the Red Sea, with a Vulnerable conservation status, and little is known about many of the more peripheral populations, some of which are thought to be close to extinction. We present a de novo high-quality genome assembly for the dugong from an individual belonging to the well-monitored Moreton Bay population in Queensland, Australia. Our assembly uses long-read PacBio HiFi sequencing and Omni-C data following the Vertebrate Genome Project pipeline to reach chromosome-level contiguity (24 chromosome-level scaffolds; 3.16 Gbp) and high completeness (97.9% complete BUSCOs). We observed relatively high genome-wide heterozygosity, which likely reflects historical population abundance before the last interglacial period, approximately 125,000 yr ago. Demographic inference suggests that dugong populations began declining as sea levels fell after the last interglacial period, likely a result of population fragmentation and habitat loss due to the exposure of seagrass meadows. We find no evidence for ongoing recent inbreeding in this individual. However, runs of homozygosity indicate some past inbreeding. Our draft genome assembly will enable range-wide assessments of genetic diversity and adaptation, facilitate effective management of dugong populations, and allow comparative genomics analyses including with other sirenians, the oldest marine mammal lineage.

Translating genomic advances into biodiversity conservation

Posted on by

Type: Journal Article

Reference: Hogg, C.J. Translating genomic advances into biodiversity conservation. Nat Rev Genet (2023). https://doi.org/10.1038/s41576-023-00671-0

Abstract

A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.

DNA methylation networks underlying mammalian traits

Posted on by

Type: Journal article

Reference: Haghani, A., et al. (2023). DNA methylation networks underlying mammalian traits. Science, 381(6658), eabq5693. https://doi.org/doi:10.1126/science.abq5693

Abstract

Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.

Universal DNA methylation age across mammalian tissues

Posted on by

Type: Journal Article

Reference: Lu, A. T., et al. (2023). Universal DNA methylation age across mammalian tissues. Nature Aging. https://doi.org/10.1038/s43587-023-00462-6

Abstract

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

Tasmanian devil cathelicidins exhibit anticancer activity against Devil Facial Tumour Disease (DFTD) cells

Posted on by

Type: Journal Article

Reference: Petrohilos, C., Patchett, A., Hogg, C.J. et al. Tasmanian devil cathelicidins exhibit anticancer activity against Devil Facial Tumour Disease (DFTD) cells. Science Report 13, 12698 (2023). doi: 10.1038/s41598-023-39901-0

Abstract

The Tasmanian devil (Sarcophilus harrisii) is endangered due to the spread of Devil Facial Tumour Disease (DFTD), a contagious cancer with no current treatment options. Here we test whether seven recently characterized Tasmanian devil cathelicidins are involved in cancer regulation. We measured DFTD cell viability in vitro following incubation with each of the seven peptides and describe the effect of each on gene expression in treated cells. Four cathelicidins (Saha-CATH3, 4, 5 and 6) were toxic to DFTD cells and caused general signs of cellular stress. The most toxic peptide (Saha-CATH5) also suppressed the ERBB and YAP1/TAZ signaling pathways, both of which have been identified as important drivers of cancer proliferation. Three cathelicidins induced inflammatory pathways in DFTD cells that may potentially recruit immune cells in vivo. This study suggests that devil cathelicidins have some anti-cancer and inflammatory functions and should be explored further to determine whether they have potential as treatment leads.

The genome sequence of the critically endangered Kroombit tinkerfrog

Posted on by

Type: Journal Article

Reference: Farquharson, K., McLennan, E., Belov, K., & Hogg, C. (2023). The genome sequence of the critically endangered Kroombit tinkerfrog (Taudactylus pleione). F1000Research, 12(845). https://doi.org/10.12688/f1000research.138571.1

Abstract

The Kroombit tinkerfrog (Taudactylus pleione) is a stream-dwelling amphibian of the Myobatrachidae family. It is listed as Critically Endangered and is at high risk of extinction due to chytridiomycosis. Here, we provide the first genome assembly of the evolutionarily distinct Taudactylus genus. We sequenced PacBio HiFi reads to assemble a high-quality long-read genome and identified the mitochondrial genome. We also generated a global transcriptome from a tadpole to improve gene annotation. The genome was 5.52 Gb in length and consisted of 4,196 contigs with a contig N50 of 8.853 Mb and an L50 of 153. This study provides the first genomic resources for the Kroombit tinkerfrog to assist in future phylogenetic, environmental DNA, conservation breeding, and disease susceptibility studies.

Adaptive Genetic Management of a Reintroduction Program from Captive Breeding to Metapopulation Management of an Arboreal Marsupial

Posted on by

Type: Journal article

Reference: Pierson, J. C., Berry, L., Alexander, L., Anson, J., Birkett, M., Kemp, L., Pascoe, B. A., Farquharson, K. A., & Hogg, C. J. (2023). Adaptive Genetic Management of a Reintroduction Program from Captive Breeding to Metapopulation Management of an Arboreal Marsupial. Diversity, 15(7), 848. https://www.mdpi.com/1424-2818/15/7/848

Abstract

The application of genetic data to conservation management programs can be hindered by the mismatch in timelines for management decisions and the acquisition of genetic data, particularly genomic sequence data that may require outsourcing. While applying genetic principles where data are absent can provide general guidelines for actions, genetic data can often fine-tune actions through adaptive management. We describe the adaptive genetic management of the establishment of a metapopulation of a small arboreal marsupial, the red-tailed phascogale (Phascogale calura). Two captive breeding programs were established as source populations, with genetic principles applied to the establishment of the first program and empirical genetic data used to guide the establishment of the second program. Genetic data from both programs were then used to allocate founders to three new populations to create a metapopulation with diversity both within and among the sites. Building and maintaining the diversity of metapopulations when recovering threatened species will reduce pressure on the original source populations and increase the resilience of the species.