Characteristics of MHC Class I Genes in House Sparrows Passer domesticus as Revealed by Long cDNA Transcripts and Amplicon Sequencing

• Published in: Journal of molecular evolution Vol. 77; no. 1-2; pp. 8 - 21
• Main Authors: Karlsson, Maria, Westerdahl, Helena
• Format: Journal Article
• Language: English
• Published: Boston Springer US 01.08.2013; Springer Nature B.V
• Subjects: Alleles; Amino Acid Sequence; Amino acids; Amplicon 454-sequencing; Animal Genetics and Genomics; Animal populations; Animals; Biologi; Biological Sciences; Biomedical and Life Sciences; Birds; cDNA; Cell Biology; Chickens; Deoxyribonucleic acid; DNA; DNA, Complementary - chemistry; Evolutionary Biology; Exons; Galliformes; Gallus gallus; Gene Order; Genetic linkage; Genomics; Histocompatibility Antigens Class I - chemistry; Histocompatibility Antigens Class I - genetics; House sparrow; Life Sciences; Linkage; MHC class I; Microbiology; Molecular Sequence Data; Natural Sciences; Naturvetenskap; Nucleic Acid Amplification Techniques; Original Article; Passer; Passer domesticus; Passeriformes; Phylogeny; Plant Genetics and Genomics; Plant Sciences; Protein Interaction Domains and Motifs; Recombination, Genetic; Selection, Genetic; Sequence Alignment; Sequence Analysis, DNA; Songbirds; Sparrows - classification; Sparrows - genetics; Sparrows - immunology; MHC class I; cDNA; Linkage; House sparrow; Amplicon 454-sequencing
• ISSN: 0022-2844; 1432-1432; 1432-1432
• DOI: 10.1007/s00239-013-9575-y

In birds the major histocompatibility complex (MHC) organization differs both among and within orders; chickens Gallus gallus of the order Galliformes have a simple arrangement, while many songbirds of the order Passeriformes have a more complex arrangement with larger numbers of MHC class I and II genes. Chicken MHC genes are found at two independent loci, classical MHC - B and non-classical MHC - Y , whereas non-classical MHC genes are yet to be verified in passerines. Here we characterize MHC class I transcripts (α1 to α3 domain) and perform amplicon sequencing using a next-generation sequencing technique on exon 3 from house sparrow Passer domesticus (a passerine) families. Then we use phylogenetic, selection, and segregation analyses to gain a better understanding of the MHC class I organization. Trees based on the α1 and α2 domain revealed a distinct cluster with short terminal branches for transcripts with a 6-bp deletion. Interestingly, this cluster was not seen in the tree based on the α3 domain. 21 exon 3 sequences were verified in a single individual and the average numbers within an individual were nine and five for sequences with and without a 6-bp deletion, respectively. All individuals had exon 3 sequences with and without a 6-bp deletion. The sequences with a 6-bp deletion have many characteristics in common with non-classical MHC, e.g., highly conserved amino acid positions were substituted compared with the other alleles, low nucleotide diversity and just a single site was subject to positive selection. However, these alleles also have characteristics that suggest they could be classical, e.g., complete linkage and absence of a distinct cluster in a tree based on the α3 domain. Thus, we cannot determine for certain whether or not the alleles with a 6-bp deletion are non-classical based on our present data. Further analyses on segregation patterns of these alleles in combination with dating the 6-bp deletion through MHC characterization across the genus Passer may solve this matter in the future.