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

Author:
  • Maria Karlsson
  • Helena Westerdahl
Publishing year: 2013
Language: English
Pages: 8-21
Publication/Series: Journal of Molecular Evolution
Volume: 77
Issue: 1-2
Document type: Journal article
Publisher: Springer

Abstract english

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.

Keywords

  • Biological Sciences
  • MHC class I
  • House sparrow
  • Amplicon 454-sequencing
  • cDNA
  • Linkage

Other

Published
  • Avian MHC genes
  • Molecular Ecology and Evolution Lab
  • ISSN: 0022-2844
Helena Westerdahl
E-mail: helena [dot] westerdahl [at] biol [dot] lu [dot] se

Senior lecturer

MEMEG

+46 46 222 36 69

E-C250

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Research group

Molecular Ecology and Evolution Lab

Projects

Doctoral students and postdocs

Research fellows

Postdocs

Luz Garcia-Longoria

PhD students, main supervisor

Samantha Mellinger

PhD students, assistant supervisor

Gustaf Ekelund Ugge

Helena Westerdahl w house sparrow