Résumé
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 (Grs and Ors,
respectively), in the process of host race formation. We used targeted
re-sequencing 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,
and a decrease in the probability of complete gene duplication or deletion
(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
Grs were over-represented 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.