Only rare classical MHC-I alleles are highly expressed in the European house sparrow

The exceptional polymorphism observed within genes of the major histocompatibility complex (MHC), a core component of the vertebrate immune system, has long fascinated biologists. The highly polymorphic classical MHC class-I (MHC-I) genes are maintained by pathogen-mediated balancing selection (PMBS), as shown by many sites subject to positive selection, while the more monomorphic MHC-I genes show signatures of purifying selection. In line with PMBS, at any point in time, rare classical MHC alleles are more likely than common classical MHC alleles to confer a selective advantage in host-pathogen interactions. Combining genomic and expression data from the blood of wild house sparrows Passer domesticus, we found that only rare classical MHC-I alleles were highly expressed, while common classical MHC-I alleles were lowly expressed or not expressed. Moreover, highly expressed rare classical MHC-I alleles had more positively selected sites, indicating exposure to stronger PMBS, compared wit..., Exon 3 of MHC class I was amplified and sequenced on the Illumina MiSeq platform from gDNA and cDNA originating from blood samples collected from 28 house sparrows (Passer domesticus) at four sites across Europe. Reads were trimmed and filtered to identify unique allele sequences in gDNA and cDNA. Alleles were classified as classical or non-classical, with non-classical alleles identified as having a 6 bp deletion. Filtered read counts were converted into allele presence/absence (1/0) for gDNA and cDNA, and cDNA read counts were designated as the expression levels for (i) nucleotide alleles (MHCI_cDNA_gDNA_nt_geno_pheno.txt) and (ii) amino acid alleles (MHCI_cDNA_gDNA_aa_geno_pheno.txt). Allele frequencies (i.e. number of individuals carrying each allele) were calculated. The numbers of unique genomic and expressed alleles were summed for each bird (MHCI_cDNA_gDNA_total_alleles_pheno.txt). Accompanying phenotypic data include country of origin (Bulgaria, Poland, Spain or Sweden) and sea..., , # Data from: Only rare classical MHC-I alleles are highly expressed in the European house sparrow

Datasets contain data on genomic and expressed diversity of the major histocompatibility (MHC) class I in European house sparrows (*Passer domesticus*). Data originates from amplicon sequencing of the exon 3 region of MHC-I in gDNA and cDNA, originating from the blood of 28 house sparrows, sampled at four sites across Europe. MHC-I alleles are classified as classical or non-classical, with non-classical alleles identified as having a 6-bp deletion. Analyses conducted included investigation of the variation in genomic and expressed MHC-I diversity, variation in MHC-I expression (probability and level of expression) in relation to allele frequency (i.e. frequency of allele in the sampled population) and variation in MHC-I expression level according to the rank order of expression level within each individual's genotype. Analyses were conducted at the level of nucleotide alleles and amino a...