High polymorphism in big defensin gene expression reveals presence–absence gene variability (PAV) in the oyster Crassostrea gigas

• Cg-BigDefs display a high interindividual polymorphism in basal mRNA expression.
• All three Cg-BigDefs are not simultaneously expressed in a single oyster.
• Lack of Cg-BigDef mRNA expression is likely due to the absence of the corresponding gene.
• First report in an invertebrate of Presence–Absence Variation affecting immune genes.

We report here the first evidence in an invertebrate, the oyster Crassostrea gigas, of a phenomenon of Presence–Absence Variation (PAV) affecting immune-related genes. We previously evidenced an extraordinary interindividual variability in the basal mRNA abundances of oyster immune genes including those coding for a family of antimicrobial peptides, the big defensins (Cg-BigDef). Cg-BigDef is a diverse family composed of three members: Cg-BigDef1 to -3. Here, we show that besides a high polymorphism in Cg-BigDef mRNA expression, not all individual oysters express simultaneously the three Cg-BigDefs. Moreover, in numerous individuals, no expression of Cg-BigDefs could be detected. Further investigation at the genomic level revealed that in individuals in which the transcription of one or all Cg-BigDefs was absent the corresponding Cg-bigdef gene was missing. In our experiments, no correlation was found between Cg-bigdef PAV and oyster capacity to survive Vibrio infections. The discovery of P-A immune genes in oysters leads to reconsider the role that the immune system plays in the individual adaptation to survive environmental, biotic and abiotic stresses.