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Contrasting segregation patterns among endogenous retroviruses across the koala population
Mette Lillie1,2, Mats Pettersson3, Patric Jern4
1Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden. Mette.Lillie@ebc.uu.se.
Communications Biology
|March 22, 2024
Summary
Koalas harbor numerous endogenous retroviruses (ERVs), including recent phaCin-β lineages. Geographic patterns reveal distinct ERV distributions, offering valuable genetic markers for conserving this endangered marsupial.
Area of Science:
- Genomics
- Virology
- Conservation Genetics
Background:
- Koalas (Phascolarctos cinereus) possess a genomic record of past retroviral epidemics as endogenous retroviruses (ERVs).
- A specific lineage, phaCin-β, exhibits recent or ongoing activity with significant insertional polymorphism within koala populations.
Purpose of the Study:
- To investigate the geographic distribution of three distinct ERV lineages (KoRV, phaCin-β, and phaCin-β-like) in koalas.
- To analyze the insertional polymorphism and frequency patterns of these ERVs across different koala populations.
Main Methods:
- Whole-genome sequencing of 430 koalas from the Koala Genome Survey.
- Identification and analysis of thousands of ERV loci across the koala population.
- Comparison of ERV patterns between northern and southern koala populations.
Main Results:
- Thousands of ERV loci were identified, with significant variation in polymorphism.
- Northern koalas showed numerous KoRV and phaCin-β integrations.
- Southern koalas exhibited higher frequencies of phaCin-β, suggesting recent activity and potential founder effects.
Conclusions:
- Koalas exhibit a substantial burden of ERVs, reflecting a long history of retrovirus-host interactions.
- The identified ERV catalogue provides novel genetic markers crucial for the conservation of endangered koalas.
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