Tag Archives: Katherine Belov

Genomics identifies koala populations at risk across eastern Australia

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Type: Journal article

Reference: McLennan, Elspeth A., Toby G. L. Kovacs, Luke W. Silver, Zhiliang Chen, Frederick R. Jaya, Simon Y. W. Ho, Katherine Belov, and Carolyn J. Hogg. 2025. “ Genomics Identifies Koala Populations at Risk across Eastern Australia.” Ecological Applications 35(1): e3062. https://doi.org/10.1002/eap.3062

Abstract

Koalas are an iconic, endangered, Australian marsupial. Disease, habitat destruction, and catastrophic mega-fires have reduced koalas to remnant patches of their former range. With increased likelihood of extreme weather events and ongoing habitat clearing across Australia, koala populations are vulnerable to further declines and isolation. Small, isolated populations are considered at risk when there is increased inbreeding, erosion of genomic diversity, and loss of adaptive potential, all of which reduce their ability to respond to prevailing threats. Here, we characterized the current genomic landscape of koalas using data from The Koala Genome Survey, a joint initiative between the Australian Federal and New South Wales Governments that aimed to provide a future-proofed baseline genomic dataset across the koala’s range in eastern Australia. We identified several regions of the continent where koalas have low genomic diversity and high inbreeding, as measured by runs of homozygosity. These populations included coastal sites along southeast Queensland and northern and mid-coast New South Wales, as well as southern New South Wales and Victoria. Analysis of genomic vulnerability to future climates revealed that northern koala populations were more at risk due to the extreme expected changes in this region, but that the adaptation required was minimal compared with other species. Our genomic analyses indicate that continued development, particularly linear infrastructure along coastal sites, and resultant habitat destruction are causing isolation and subsequent genomic erosion across many koala populations. Habitat protection and the formation of corridors must be employed for all koala populations to maintain current levels of diversity. For highly isolated koala populations, active management may be the only way to improve genomic diversity in the short term. If koalas are to be conserved for future generations, reversing their genomic isolation must be a priority in conservation planning.

Bioactive components in the marsupial pouch and milk

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Type: Journal article

Reference: Jayamanna Mohottige MW, Gardner CE, Nye-Wood MG, Farquharson KA, Juhász A, Belov K, Hogg CJ, Peel E, Colgrave ML. Bioactive components in the marsupial pouch and milk. Nutr Res Rev. 2024 Nov 18:1-12. doi: 10.1017/S0954422424000313.

Abstract

Marsupials give birth to immunologically naïve young after a relatively short gestation period compared with eutherians. Consequently, the joey relies significantly on maternal protection, which is the focus of the present review. The milk and the pouch environment are essential contributors to maternal protection for the healthy development of joeys. In this review, we discuss bioactive components found in the marsupial pouch and milk that form cornerstones of maternal protection. These bioactive components include immune cells, immunoglobulins, the S100 family of calcium-binding proteins, lysozymes, whey proteins, antimicrobial peptides and other immune proteins. Furthermore, we investigated the possibility of the presence of plurifunctional components in milk and pouches that are potentially bioactive. These compounds include caseins, vitamins and minerals, oligosaccharides, lipids and microRNAs. Where applicable, this review addresses variability in bioactive components during different phases of lactation, designed to fulfil the immunological needs of the growing pouch young. Yet, there are numerous additional research opportunities to pursue, including uncovering novel bioactive components and investigating their modes of action, dynamics, stability and ability to penetrate the gut epithelium to facilitate systemic effects.

Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas

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Type: Journal article

Reference: Silver LW, McLennan EA, Beaman J, da Silva KB, Timms P, Hogg CJ, Belov K. Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas. Immunogenetics. 2024 Dec;76(5-6):381-395. doi: 10.1007/s00251-024-01356-6

Abstract

Conservation genomics can greatly improve conservation outcomes of threatened populations, including those impacted by disease. Understanding diversity within immune gene families, including the major histocompatibility complex (MHC) and toll-like receptors (TLR), is important due to the role they play in disease resilience and susceptibility. With recent advancements in sequencing technologies and bioinformatic tools, the cost of generating high-quality sequence data has significantly decreased and made it possible to investigate diversity across entire gene families in large numbers of individuals compared to investigating only a few genes or a few populations previously. Here, we use the koala as a case study for investigating functional diversity across populations. We utilised previous target enrichment data and 438 whole genomes to firstly, determine the level of sequencing depth required to investigate MHC diversity and, secondly, determine the current level of diversity in MHC genes in koala populations. We determined for low complexity, conserved genes such as TLR genes 10 × sequencing depth is sufficient to reliably genotype more than 90% of variants, whereas for complex genes such as the MHC greater than 20 × and preferably 30 × sequencing depth is required. We used whole genome data to identify 270 biallelic SNPs across 24 MHC genes as well as copy number variation (CNV) within class I and class II genes and conduct supertype analysis. Overall, we have provided a bioinformatic workflow for investigating variation in a complex immune gene family from whole genome sequencing data and determined current levels of diversity within koala MHC genes.

A genomic framework to assist conservation breeding and translocation success: A case study of a critically endangered turtle

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Type: Journal article

Reference: Nelson, H. V., Farquharson, K. A., Georges, A., McLennan, E. A., DeGabriel, J. L., Giese, M., Ormond, C., McFadden, M., Skidmore, A., Prangell, J., Belov, K., & Hogg, C. J. (2024). A genomic framework to assist conservation breeding and translocation success: A case study of a critically endangered turtle. Conservation Science and Practice, 6(10), e13204. https://doi.org/10.1111/csp2.13204

Abstract

Conservation breeding programs are an effective approach to addressing biodiversity loss. Captive populations are managed to maintain genetic diversity, yet there remains an “implementation gap” in effectively translating molecular genetic data into management. Technological advancements are facilitating rapid generation of genetic data, increasing accessibility for breeding programs. In 2010, Frankham and colleagues proposed a six-stage process for establishing successful conservation breeding and release programs. Here, we describe the conservation breeding program for the critically endangered Bellinger River turtle (Myuchelys georgesi) and characterize the value of genetic sampling for informing management actions. By generating a chromosome-level genome and population genetic data, we investigated past and present diversity and assessed relatedness among captive founders. We present a framework modeled on Frankham and colleagues six stages to assist managers in implementing genetic data into actionable conservation strategies. This framework, and worked case study, for managers aims to better guide implementation of genetic approaches into conservation breeding programs.

Hijacking of N-fixing legume albumin-1 genes enables the cyclization and stabilization of defense peptides

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Article: Journal article

Reference: Gilding, E.K., Jackson, M.A., Nguyen, L.T.T. et al. Hijacking of N-fixing legume albumin-1 genes enables the cyclization and stabilization of defense peptides. Nat Commun 15, 6565 (2024). https://doi.org/10.1038/s41467-024-50742-x

Abstract

The legume albumin-1 gene family, arising after nodulation, encodes linear a- and b-chain peptides for nutrient storage and defense. Intriguingly, in one prominent legume, Clitoria ternatea, the b-chains are replaced by domains producing ultra-stable cyclic peptides called cyclotides. The mechanism of this gene hijacking is until now unknown. Cyclotides require recruitment of ligase-type asparaginyl endopeptidases (AEPs) for maturation (cyclization), necessitating co-evolution of two gene families. Here we compare a chromosome-level C. ternatea genome with grain legumes to reveal an 8 to 40-fold expansion of the albumin-1 gene family, enabling the additional loci to undergo diversification. Iterative rounds of albumin-1 duplication and diversification create four albumin-1 enriched genomic islands encoding cyclotides, where they are physically grouped by similar pI and net charge values. We identify an ancestral hydrolytic AEP that exhibits neofunctionalization and multiple duplication events to yield two ligase-type AEPs. We propose cyclotides arise by convergence in C. ternatea where their presence enhances defense from biotic attack, thus increasing fitness compared to lineages with linear b-chains and ultimately driving the replacement of b-chains with cyclotides.

Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

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Type: Journal article

Reference: Hogg, C.J., Edwards, R.J., Farquharson, K.A. et al. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 8, 1311–1326 (2024). https://doi.org/10.1038/s41559-024-02436-2

Abstract

Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom–bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.

The future is here: an easy-to-use toolkit for integrating genetics into conservation management

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Type: Journal article

Reference: Hogg, C.J., Farquharson, K.A., Brandies, P., Silver, L.W., Ottewell, K., McLennan, E.A., Richmond, S. and Belov, K. (2025), The future is here: an easy-to-use toolkit for integrating genetics into conservation management. Anim Conserv, 28: 93-103. https://doi.org/10.1111/acv.12971

Abstract

Over the past decade, the development of genetic and genomic tools for conservation management has come forward in leaps and bounds. Once considered a ‘nice to have’, genetic data are fast becoming an essential tool for informing and managing translocations. However, due to the complexity of the field, easily using genetic data for decision-making and monitoring remains beyond the reach of most managers and conservation biologists. In May 2020, we launched the Threatened Species Initiative (TSI), a programme designed to generate genomic resources for Australia’s threatened species. Critical to the project is not only the generation of reference genomes and population genetic data but an online toolkit for conservation managers. The toolkit is a ‘one stop shop’ from collecting samples, to generating and analysing genetic data, to an easily interpretable genetic management report. A series of workflows and pipelines have been developed, including the TSI Biodiversity Portal, that uses point and click web interfaces to easily transfer raw sequence data and assemble genomes, transcriptomes and soon population genetics for management decisions. Here we present how the current toolkit works and provide case study examples for how it is being used to inform translocations and the management of threatened species.

Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II

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Type: Journal article

Reference: Luke W Silver, Carolyn J Hogg, Katherine Belov, Plethora of New Marsupial Genomes Informs Our Knowledge of Marsupial MHC Class II, Genome Biology and Evolution, Volume 16, Issue 8, August 2024, evae156, https://doi.org/10.1093/gbe/evae156

Abstract

The major histocompatibility complex (MHC) plays a vital role in the vertebrate immune system due to its role in infection, disease and autoimmunity, or recognition of “self”. The marsupial MHC class II genes show divergence from eutherian MHC class II genes and are a unique taxon of therian mammals that give birth to altricial and immunologically naive young providing an opportune study system for investigating evolution of the immune system. Additionally, the MHC in marsupials has been implicated in disease associations, including susceptibility to Chlamydia pecorum infection in koalas. Due to the complexity of the gene family, automated annotation is not possible so here we manually annotate 384 class II MHC genes in 29 marsupial species. We find losses of key components of the marsupial MHC repertoire in the Dasyuromorphia order and the Pseudochiridae family. We perform PGLS analysis to show the gene losses we find are true gene losses and not artifacts of unresolved genome assembly. We investigate the associations between the number of loci and life history traits, including lifespan and reproductive output in lineages of marsupials and hypothesize that gene loss may be linked to the energetic cost and tradeoffs associated with pregnancy and reproduction. We found support for litter size being a significant predictor of the number of DBA and DBB loci, indicating a tradeoff between the energetic requirements of immunity and reproduction. Additionally, we highlight the increased susceptibility of Dasyuridae species to neoplasia and a potential link to MHC gene loss. Finally, these annotations provide a valuable resource to the immunogenetics research community to move forward and further investigate diversity in MHC genes in marsupials.

Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females

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Type: Journal article

Reference: Ockert, L.E., McLennan, E.A., Fox, S. et al. Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females. Sci Rep 14, 15188 (2024). https://doi.org/10.1038/s41598-024-66097-8

Abstract

Wildlife harbour a diverse range of microorganisms that affect their health and development. Marsupials are born immunologically naïve and physiologically underdeveloped, with primary development occurring inside a pouch. Secretion of immunological compounds and antimicrobial peptides in the epithelial lining of the female’s pouch, pouch young skin, and through the milk, are thought to boost the neonate’s immune system and potentially alter the pouch skin microbiome. Here, using 16S rRNA amplicon sequencing, we characterised the Tasmanian devil pouch skin microbiome from 25 lactating and 30 non-lactating wild females to describe and compare across these reproductive stages. We found that the lactating pouch skin microbiome had significantly lower amplicon sequence variant richness and diversity than non-lactating pouches, however there was no overall dissimilarity in community structure between lactating and non-lactating pouches. The top five phyla were found to be consistent between both reproductive stages, with over 85% of the microbiome being comprised of Firmicutes, Proteobacteria, Fusobacteriota, Actinobacteriota, and Bacteroidota. The most abundant taxa remained consistent across all taxonomic ranks between lactating and non-lactating pouch types. This suggests that any potential immunological compounds or antimicrobial peptide secretions did not significantly influence the main community members. Of the more than 16,000 total identified amplicon sequence variants, 25 were recognised as differentially abundant between lactating and non-lactating pouches. It is proposed that the secretion of antimicrobial peptides in the pouch act to modulate these microbial communities. This study identifies candidate bacterial clades on which to test the activity of Tasmanian devil antimicrobial peptides and their role in pouch young protection, which in turn may lead to future therapeutic development for human diseases.

Characterisation of defensins across the marsupial family tree

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Type: Journal Article

Reference: Peel, E., Hogg, C. and Belov, K., 2024. Characterisation of defensins across the marsupial family tree. Developmental & Comparative Immunology, p.105207. https://doi.org/10.1016/j.dci.2024.105207

Abstract

Defensins are antimicrobial peptides involved in innate immunity, and gene number differs amongst eutherian mammals. Few studies have investigated defensins in marsupials, despite their potential involvement in immunological protection of altricial young. Here we use recently sequenced marsupial genomes and transcriptomes to annotate defensins in nine species across the marsupial family tree. We characterised 35 alpha and 286 beta defensins; gene number differed between species, although Dasyuromorphs had the largest repertoire. Defensins were encoded in three gene clusters within the genome, syntenic to eutherians, and were expressed in the pouch and mammary gland. Marsupial beta defensins were closely related to eutherians, however marsupial alpha defensins were more divergent. We identified marsupial orthologs of human DEFB3 and 6, and several marsupial-specific beta defensin lineages which may have novel functions. Marsupial predicted mature peptides were highly variable in length and sequence composition. We propose candidate peptides for future testing to elucidate the function of marsupial defensins.