Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia

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cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationCommonwealth Scientific and Industrial Research Organisation, Australiaen
cg.contributor.affiliationDeakin Universityen
cg.contributor.affiliationAustralian National Universityen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationNorthern Australia Quarantine Strategyen
cg.contributor.affiliationCharles Darwin Universityen
cg.contributor.affiliationNew South Wales Department of Primary Industriesen
cg.contributor.donorDepartment of Foreign Affairs and Trade, Australiaen
cg.coverage.countryAustralia
cg.coverage.iso3166-alpha2AU
cg.coverage.regionAustralia and New Zealand
cg.creator.identifierAppolinaire Djikeng: 0000-0001-9271-3419
cg.creator.identifierStephen J Kemp: 0000-0003-4041-1720
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1186/s12864-016-3124-1en
cg.isijournalISI Journalen
cg.issn1471-2164en
cg.issue1en
cg.journalBMC Genomicsen
cg.reviewStatusPeer Reviewen
cg.subject.ilriANIMAL DISEASESen
cg.subject.ilriEPIDEMIOLOGYen
cg.subject.ilriGENETICSen
cg.subject.ilriLIVESTOCKen
cg.volume17en
dc.contributor.authorOnyango, M.G.en
dc.contributor.authorAitken, N.C.en
dc.contributor.authorJack, C.en
dc.contributor.authorChuah, A.en
dc.contributor.authorOguya, J.en
dc.contributor.authorDjikeng, Appolinaireen
dc.contributor.authorKemp, Stephen J.en
dc.contributor.authorBellis, G.A.en
dc.contributor.authorNicholas, A.en
dc.contributor.authorWalker, P.J.en
dc.contributor.authorDuchemin, J.B.en
dc.date.accessioned2017-07-18T08:22:03Zen
dc.date.available2017-07-18T08:22:03Zen
dc.identifier.urihttps://hdl.handle.net/10568/82801
dc.titleGenotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australiaen
dcterms.abstractBACKGROUND: The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges. RESULTS: This study employed the GBS method to isolate SNP markers de novo from whole genome amplified Culicoides brevitarsis genomic DNA. The individuals were collected from regions representing two different Australian patterns of BTV strain distribution: the Northern Territory (NT) and the east coast. We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. Two loci showed a very strong signal for selection and were unique to the NT population. Bayesian analysis with STRUCTURE indicated a possible two-population cluster. CONCLUSIONS: The results suggest that genotyping vectors with high density markers in combination with biological and environmental data is useful. However, more extensive sampling over a wider spatial and temporal range is needed. The presence of sub-structure in populations and loci under natural selection indicates the need for further investigation of the role of vectors in shaping the two Australian systems of BTV transmission. The described workflow is transferable to genotyping of small, non-model organisms, including arthropod vectors of pathogens of economic and medical importance.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2016-09-30
dcterms.bibliographicCitationOnyango, M.G., Aitken, N.C., Jack, C., Chuah, A., Oguya, J., Djikeng, A., Kemp, S., Bellis, G.A., Nicholas, A., Walker, P.J. and Duchemin, J.B. 2016. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia. BMC Genomics 17(1):769.en
dcterms.issued2016-12
dcterms.languageen
dcterms.licenseCopyrighted; all rights reserved
dcterms.publisherSpringeren
dcterms.subjectanimal diseasesen
dcterms.subjectanimal geneticsen
dcterms.subjectepidemiologyen
dcterms.subjectlivestocken
dcterms.typeJournal Article

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