Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Jun;31(12):3286-3303.
doi: 10.1111/mec.16493. Epub 2022 May 17.

A targeted approach to investigating immune genes of an iconic Australian marsupial

Luke W Silver  1 , Yuanyuan Cheng  1 , Bonnie L Quigley  2 , Amy Robbins  2   3 , Peter Timms  2 , Carolyn J Hogg  1 , Katherine Belov  1
Affiliations

A targeted approach to investigating immune genes of an iconic Australian marsupial

Luke W Silver et al. Mol Ecol. 2022 Jun.

Abstract

Disease is a contributing factor to the decline of wildlife populations across the globe. Koalas, iconic yet declining Australian marsupials, are predominantly impacted by two pathogens, Chlamydia and koala retrovirus. Chlamydia is an obligate intracellular bacterium and one of the most widespread sexually transmitted infections in humans worldwide. In koalas, Chlamydia infections can present as asymptomatic or can cause a range of ocular and urogenital disease signs, such as conjunctivitis, cystitis and infertility. In this study, we looked at differences in response to Chlamydia in two northern populations of koalas using a targeted gene sequencing of 1209 immune genes in addition to genome-wide reduced representation data. We identified two MHC Class I genes associated with Chlamydia disease progression as well as 25 single nucleotide polymorphisms across 17 genes that were associated with resolution of Chlamydia infection. These genes are involved in the innate immune response (TLR5) and defence (TLR5, IFNγ, SERPINE1, STAT2 and STX4). This study deepens our understanding of the role that genetics plays in disease progression in koalas and leads into future work that will use whole genome resequencing of a larger sample set to investigate in greater detail regions identified in this study. Elucidation of the role of host genetics in disease progression and resolution in koalas will directly contribute to better design of Chlamydia vaccines and management of koala populations which have recently been listed as "endangered."

Keywords: Chlamydia; GWAS; conservation genomics; koala; wildlife disease.

PubMed Disclaimer

Conflict of interest statement

The authors have no conflicts of interest to disclose.

Figures

FIGURE 1
FIGURE 1
(a) PCoA plot produced using genome‐wide neutral SNPs from 41 sequenced individuals, with individuals labelled by whether they were able to resolve a Chlamydia infection (resolvers—purple triangles) or not (nonresolvers—black circles). (b) PCoA plot produced using genome‐wide neutral SNPs from 41 sequenced individuals, with individuals labelled by study population, either Moreton Bay or Hidden Vale. (c) PCoA plot produced using biallelic SNPs from targeted immune genes in 43 sequenced individuals, with individuals labelled by whether they were able to resolve a Chlamydia infection (resolvers) or not (nonresolvers). (d) PCoA plot produced using biallelic SNPs from targeted immune genes in 43 sequenced individuals, with individuals labelled by study population, either Moreton Bay (blue triangles) or Hidden Vale (red circles)
FIGURE 2
FIGURE 2
Genomic location of the 19 MHC Class I and 16 MHC Class II genes annotated, with yellow bars indicating which genes were included in our target probe set. Created with BioRender.com
FIGURE 3
FIGURE 3
Boxplot displaying the proportion of heterozygotes (PHt) at Hidden Vale and Moreton Bay determined from immune gene SNPs (red) and genome‐wide neutral SNPs (blue). Whiskers mark the “minimum” (1Q − 1.5 × IQR) and “maximum” (3Q + 1.5 × IQR), with outliers shown as dots
FIGURE 4
FIGURE 4
Interaction of four genes (IFNγ, RAB35, STAT2 andTLR5) with GO terms, determined using GOnet (Pomaznoy et al., 2018), with genes in orange circles and GO terms in blue rectangles. For the full interaction plot, see Figure S3
FIGURE 5
FIGURE 5
Bar plot representing the differences in proportion of each allele present between koalas that resolved a Chlamydia infection and koalas that did not resolve an infection in the genes UA and UC
See this image and copyright information in PMC

References

    1. Adams‐Hosking, C. , McBride, M. F. , Baxter, G. , Burgman, M. , de Villiers, D. , Kavanagh, R. , & McAlpine, C. A. (2016). Use of expert knowledge to elicit population trends for the koala (Phascolarctos cinereus). Diversity and Distributions, 22(3), 249–262. 10.1111/ddi.12400 - DOI
    1. Akira, S. , Uematsu, S. , & Takeuchi, O. (2006). Pathogen recognition and innate immunity. Cell, 124(4), 783–801. 10.1016/j.cell.2006.02.015 - DOI - PubMed
    1. Altschul, S. F. , Gish, W. , Miller, W. , Myers, E. W. , & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. 10.1016/S0022-2836(05)80360-2 - DOI - PubMed
    1. Ashburner, M. , Ball, C. A. , Blake, J. A. , Botstein, D. , Butler, H. , Cherry, J. M. , Davis, A. P. , Dolinski, K. , Dwight, S. S. , Eppig, J. T. , Harris, M. A. , Hill, D. P. , Issel‐Tarver, L. , Kasarskis, A. , Lewis, S. , Matese, J. C. , Richardson, J. E. , Ringwald, M. , Rubin, G. M. , & Sherlock, G. (2000). Gene ontology: tool for the unification of biology. Nature Genetics, 25(1), 25–29. 10.1038/75556 - DOI - PMC - PubMed
    1. Axelsson, E. , Ratnakumar, A. , Arendt, M.‐L. , Maqbool, K. , Webster, M. T. , Perloski, M. , Liberg, O. , Arnemo, J. M. , Hedhammar, Å. , & Lindblad‐Toh, K. (2013). The genomic signature of dog domestication reveals adaptation to a starch‐rich diet. Nature, 495(7441), 360–364. 10.1038/nature11837 - DOI - PubMed

Publication types

Substances