Evolutionary dynamics of an expressed MHC class IIβ beta locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing

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Mulder, Kevin P.Smithsonian Conservat Biol Inst, Ctr Conservat Genom, Natl Zool Pk.;CIBIO InBIO, Res Ctr Biodivers & Genet Resources. (author)

Evolutionary dynamics of an expressed MHC class IIβ beta locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing

Article/chapterEnglish2017

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Oxford :Elsevier,2017
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LIBRIS-ID:oai:DiVA.org:uu-330525
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-330525URI
https://doi.org/10.1016/j.dci.2017.05.022DOI

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Language:English
Summary in:English

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The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and "disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class II beta chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.

Subject headings and genre

NATURVETENSKAP Biologi Zoologi hsv//swe
NATURAL SCIENCES Biological Sciences Zoology hsv//eng
NATURVETENSKAP Biologi Immunologi hsv//swe
NATURAL SCIENCES Biological Sciences Immunology hsv//eng
MHC class II beta
Ranidae
Amplicon primers
Illumina
454
Lithobates
Rana
Pelophylax
Odorrana

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Cortazar-Chinarro, MariaUppsala universitet,Zooekologi(Swepub:uu)marco507 (author)
Harris, D. JamesCIBIO InBIO, Res Ctr Biodivers & Genet Resources. (author)
Crottini, AngelicaCIBIO InBIO, Res Ctr Biodivers & Genet Resources. (author)
Grant, Evan H. CampbellUS Geol Survey, Patuxent Wildlife Res Ctr, SO Conte Anadromous Fish Res Lab. (author)
Fleischer, Robert C.Smithsonian Conservat Biol Inst, Ctr Conservat Genom, Natl Zool Pk. (author)
Savage, Anna E.Smithsonian Conservat Biol Inst, Ctr Conservat Genom, Natl Zool Pk.;Univ Cent Florida, Dept Biol. (author)
Smithsonian Conservat Biol Inst, Ctr Conservat Genom, Natl Zool Pk.;CIBIO InBIO, Res Ctr Biodivers & Genet Resources.Zooekologi (creator_code:org_t)

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In:Developmental and Comparative ImmunologyOxford : Elsevier76, s. 177-1880145-305X1879-0089

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Zoology

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Immunology

Articles in the publication: Developmental an ...

By the university: Uppsala University

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