Tag Archives: Immune genes

post

Academic Adventures to the Other Side of the Globe

Posted on by

by Luke Silver (Post-doc)

In August of 2024 I had the exciting opportunity to undertake a three-month research stay in the Institute of Evolutionary Ecology and Conservation Genomics at Ulm University. So how did this come about?

Professor Simone Sommer was one of my thesis reviewers and she reached out to Kathy and Carolyn with an opportunity to combine my skillset in genomes and MHC annotation with some newly generated bat sequences. So at the start of August, I departed Sydney for an almost 30 hour journey to the city of Ulm (about 1 hour west of Munich) in southern Germany. Upon arrival at Ulm train station, I was met by a postdoc Dr Dominik Melville who showed me to my accommodation for the next three months. With no German language knowledge, I headed to the supermarket and managed to annoy the person at the register by not pre-weighing my fruits and vegetables – just one of many times that having some German language skills would have come in handy.

The purpose of my visit was to manually annotate genes of a crucial immune gene family known as the major histocompatibility complex (MHC) in bats. These genes form molecules with are expressed on cell surfaces and are responsible for detecting self and non -self and presenting foreign pathogen derived peptides to other cells of the immune system. We were able to leverage the recently released data from phase 1 of the Bat1K project (a consortium that aims to sequence the genomes of all living bat species around the world).

I also managed to find time to sample plenty of the local delicacies of beer and pretzels  and to travel in the local area including to the beautiful Lake Konstanz, Stuttgart, Nuremberg, Vienna, Salzburg and Prague. This is just a small example of how science can lead to new and exciting experiences and opportunities.

Luke Silver

Dr Luke Silver’s research is focused on generating and using genomic and transcriptomic resources for threatened Australian species. He used these resources to investigate the evolution of the immune system and study how diversity within immune genes is linked to disease traits. He has experience in characterisation of complex immune gene families, in particular the major histocompatibility complex which is a key component of the adaptive immune system

@LukeSilver20

AMPed Up Immunity: 418 Whole Genomes Reveal Intraspecific Diversity of Koala Antimicrobial Peptides

Posted on by

Type: Journal article

Reference: Petrohilos C, Peel E, Silver LW, Belov K, Hogg CJ. AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides. Immunogenetics. 2025 Jan 8;77(1):11. doi: 10.1007/s00251-024-01368-2.

Abstract

Characterising functional diversity is a vital element to understanding a species’ immune function, yet many immunogenetic studies in non-model organisms tend to focus on only one or two gene families such as the major histocompatibility complex (MHC) or toll-like receptors (TLR). Another interesting component of the eukaryotic innate immune system is the antimicrobial peptides (AMPs). The two major groups of mammalian AMPs are cathelicidins and defensins, with the former having undergone species-specific expansions in marsupials. Here, we utilised data from 418 koala whole genomes to undertake the first comprehensive analysis of AMP diversity across a mammalian wildlife species’ range. Overall, allelic diversity was lower than other immune gene families such as MHC, suggesting that AMPs are more conserved, although balancing selection was observed in PhciDEFB12. Some non-synonymous SNPs in the active peptide are predicted to change AMP function through stop gains, change in structure, and increase in peptide charge. Copy number variants (CNVs) were observed in two defensins and one cathelicidin. Interestingly, the most common CNV was the duplication of PhciCATH5, a cathelicidin with activity against chlamydia, which was more common in the southern part of the species range than the north. AMP copy number is correlated with expression levels, so we hypothesise that there is a selective pressure from chlamydia for duplications in PhciCATH5. Future studies should use phenotypic metadata to assess the functional impacts of this gene duplication.

Spatial variation in toll-like receptor diversity in koala populations across their geographic distribution

Posted on by

Type: Journal article

Reference: Cui J, Batley KC, Silver LW, McLennan EA, Hogg CJ, Belov K. Spatial variation in toll-like receptor diversity in koala populations across their geographic distribution. Immunogenetics. 2024 Nov 30;77(1):5. doi: 10.1007/s00251-024-01365-5

Abstract

The koala (Phascolarctos cinereus) is an iconic Australian species that is listed as endangered in the northern parts of its range due to loss of habitat, disease, and road deaths. Diseases contribute significantly to the decline of koala populations, primarily Chlamydia and koala retrovirus. The distribution of these diseases across the species’ range, however, is not even. Toll-like receptors (TLRs) play a crucial role in innate immunity by recognising and responding to various pathogens. Variations in TLR genes can influence an individual’s susceptibility or resistance to infectious diseases. The aim of this study was to identify koala TLR diversity across the east coast of Australia using 413 re-sequenced genomes at 30 × coverage. We identified 45 single-nucleotide polymorphisms (SNP) leading to 51 alleles within ten TLR genes. Our results show that the diversity of TLR genes in the koala forms four distinct genetic groups, which are consistent with the diversity of the koala major histocompatibility complex (MHC), another key immune gene family. The bioinformatics approach presented here has broad applicability to other threatened species with existing genomic resources.