Periodic Reporting for period 4 - Optimal-Immunity (Optimal diversity in immunity – to overcome pathogens and maximize fitness; moving from correlative associations to a more mechanistic understanding using wild songbirds.)
Reporting period: 2020-10-01 to 2021-09-30
2. Gene-expression - We have done RNASeq and IsoSeq to study full gene expression in both great reed warbler and house sparrow, and amplicon sequencing (MiSeq, local pipeline at LU) has been done to specifically study MHC-I gene expression in great reed warbler and house sparrow. MHC expression differs significantly between different MHC gene copies in songbirds and strong expression patterns are associated with MHC gene type. Moreover, the relative MHC expression in songbirds varies between bird families, suggesting that MHC diversity in genomic DNA overestimates the expressed diversity in some bird families, as shown in our recent publication.
3. Proteins – The crystal structure of the great reed warbler MHC-I protein Acar_3 has been characterized with high resolution with three different antigens and it unraveled an interesting antigen presenting properties that partly agrees and partly disagrees with antigen binding of classical human MHC proteins, and a manuscript is written, and planned for submission early 2022.
4. Host-pathogen interactions have been studied both in natural populations (great reed warblers in Lake Kvismaren Sweden and in house sparrows across Europe) and in experimental set-ups (house sparrows). The seasonal variation in diversity and prevalence of avian malaria varied between locations in house sparrows, as shown in our recent publication, and tended to be highest in mid-spring and early Autumn. The diversity and expression of MHC genes shows interesting patterns across Europe and our results will be submitted shortly. The house sparrow work has enrolled a large number of collaborators across Europe and I am very grateful for their engagement in my studies of MHC and avian malaria.
Maria Strandh, employed in my project, has unraveled that repetitive elements are most likely the drivers of the highly duplicated MHC region in great reed warblers. She has developed bioinformatic pipelines together with Verena Kutschera at SciLifeLab to study the distribution of repetitive elements in the entire genome, an up-coming and most likely important parameter in studies of structural genetic variation.
SciLifeLab offered me to run an optical genome map using Irys long-range next-generation technique (Bionano genomics) at an extremely low cost since they thought that we were producing a really high quality genome for the great reed warbler and both me and Maria Strandh have independently been invited to talk at the workshops at SciLifeLab.
We have had progress in the protein work on MHC-I in great reed warblers and I hope that we have a pipeline for the future where antigen binding of MHC-I can be studied, not only in great reed warblers but also in other birds.