title: Dynamics of copy number variation in host races of the pea aphid.
abstract: Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host-plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Gr and Or, respectively), in the process of host race formation. We used targeted resequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors. We also observed a decrease in the gene probability of being completely duplicated or deleted (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Gr were overrepresented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom l.duvaux@sheffield.ac.uk.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Duvaux
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.
authors.forename: Quentin
authors.initials: Q
authors.lastname: Geissmann
authors.affiliation: Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Karim
authors.initials: K
authors.lastname: Gharbi
authors.affiliation: Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, United Kingdom.
authors.forename: Jing-Jiang
authors.initials: JJ
authors.lastname: Zhou
authors.affiliation: Department of Biology, University of York, York, United Kingdom.
authors.forename: Julia
authors.initials: J
authors.lastname: Ferrari
authors.affiliation: Institut des Sciences de l'Evolution (UMR 5554), CNRS, IRD, Université Montpellier 2, Montpellier, France.
authors.forename: Carole M
authors.initials: CM
authors.lastname: Smadja
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom Sven Lovén Centre for Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden.
authors.forename: Roger K
authors.initials: RK
authors.lastname: Butlin
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D001042:Aphids / Q000145:classification* / Q000235:genetics* / Q000502:physiology; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D019143:Evolution, Molecular; D007887:Fabaceae / Q000145:classification / Q000502:physiology*; D049810:Genetic Speciation; D014644:Genetic Variation; D049750:Genome, Insect; D059014:High-Throughput Nucleotide Sequencing; D019476:Insect Proteins / Q000235:genetics*; D010802:Phylogeny; D018035:Receptors, Odorant / Q000235:genetics; D017422:Sequence Analysis, DNA; D013559:Symbiosis
chemical_list: D019476:Insect Proteins; D018035:Receptors, Odorant
keywords: Acyrthosiphon pisum; P450; adaptation; chemosensory genes; gene duplication; gene family evolution; speciation; targeted resequencing