Tag Archives: MHC

Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot

Posted on by

Type: Journal article

Reference: Silver LW, Farquharson KA, Peel E, Gilbert MTP, Belov K, Morales HE, Hogg CJ. Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot. Mol Ecol. 2025 Mar 25:e17746. doi: 10.1111/mec.17746.

Abstract

Loss of genetic diversity threatens a species’ adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.

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

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

Posted on by

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.