title: Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia.|School of Medicine, Deakin University, 75 Pidgons Road, Waurn Ponds, 3216, VIC, Australia.
authors.forename: Maria G
authors.initials: MG
authors.lastname: Onyango
authors.affiliation: Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.
authors.forename: Nicola C
authors.initials: NC
authors.lastname: Aitken
authors.affiliation: The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.
authors.forename: Cameron
authors.initials: C
authors.lastname: Jack
authors.affiliation: The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.
authors.forename: Aaron
authors.initials: A
authors.lastname: Chuah
authors.affiliation: International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya.
authors.forename: James
authors.initials: J
authors.lastname: Oguya
authors.affiliation: International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya.|Biosciences eastern and central Africa-ILRI Hub (BecA-ILRI Hub), ILRI, PO Box 30709, 00100, Nairobi, Kenya.
authors.forename: Appolinaire
authors.initials: A
authors.lastname: Djikeng
authors.affiliation: International Livestock Research Institute (ILRI), P.O. Box 30709, 00100, Nairobi, Kenya.
authors.forename: Steve
authors.initials: S
authors.lastname: Kemp
authors.affiliation: Northern Australia Quarantine Strategy, 1 Pederson Road, Marrara, 0812, NT, Australia.|Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, 0909, NT, Australia.
authors.forename: Glenn A
authors.initials: GA
authors.lastname: Bellis
authors.affiliation: NSW Department of Primary Industries, Biosecurity, 4 Marsden Park Road, Calala, 2340, NSW, Australia.
authors.forename: Adrian
authors.initials: A
authors.lastname: Nicholas
authors.affiliation: CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Walker
authors.affiliation: CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portalington Road, Geelong, 3220, VIC, Australia. Jean-Bernard.Duchemin@csiro.au.
authors.forename: Jean-Bernard
authors.identifier: 0000-0001-5044-4855
authors.initials: JB
authors.lastname: Duchemin
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002519:Ceratopogonidae / Q000235:genetics*; D003576:Electron Transport Complex IV / Q000235:genetics; D015723:Gene Library; D050259:Genes, Mitochondrial; D005828:Genetics, Population; D049750:Genome, Insect; D023281:Genomics / Q000379:methods; D005838:Genotype; D006239:Haplotypes; D015876:Northern Territory; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic
chemical_list: D003576:Electron Transport Complex IV
keywords: Australia; Bluetongue virus; Culicoides brevitarsis; GBS; SNPs