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

Abstract

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.

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

“…In spite of the growing number of reports of pan-genomes in eukaryotes and the recent extension of such investigations to human populations (32), so far the impact of PAV on the intraspecific diversity of animals has been presumed to be minimal, and sometimes linked to the development of pathologies (38). To the best of our knowledge, PAV has been only marginally explored in bivalves as a phenomenon linked to gene families involved in immune functions, i.e., big defensins in Crassostrea gigas (39) and myticalins in M. galloprovincialis (40). Therefore, this is the first study to report the widespread occurrence of PAV at a whole genome scale in metazoans, and the very first report of a pan-genome in the animal kingdom.…”

The new insights into the oyster antimicrobial defense: Cellular, molecular and genetic view

“…In addition, Cg-BigDef expression could not be detected in 39 individuals. Further analyses at genome level revealed that this lack of expression was likely associated to the absence of encoding Cg-bigdef sequences [129] as previously observed for Cg-prps [113]. In such an extreme case of CNV, known as Presence-Absence Variations (PAV), large DNA segment present in some individuals can be entirely missing in others [131].…”

“…Indubitably, analyses performed at individual level may give new light on the genetic bases of oyster immune response and reveal its diversity and complexity. From these studies it is also clear that AMP-encoding genes show a great interindividual variability of expression, as shown for Cg-defhs, Cg-prps, Cg-bpi and Cg-bigdefs [40,113,129].…”

“…No relationship was observed between the Presence-Absence of Cg-bigdefs and the capacity of the oysters to survive experimental Vibrio infections [129]. In plants, it is assumed that PAVs may generate new pathogen resistances but most of all that it could contribute to individual adaptation to environmental stresses [136].…”

The Effects of 4-Nonylphenol on the Immune Response of The Pacific Oyster, Crassostrea Gigas, Following Bacterial Infection (Vibrio Campbellii)

“…That being said, Rosa et al (2011) also reported extreme variability in transcript abundances for Cg-bigdef1, Cg-bigdef2 and Cg-bigdef3 in hemocytes despite analyzing RNA from pooled (n=10 oysters) hemolymph samples. This variability has since been attributed to a high level of gene sequence polymorphisms in oysters (Hedgecock et al, 2004;Sauvage et al, 2007), which is particularly high for the Cg-defhs and Cg-bigdefs (Schmitt et al, 2013;Rosa et al, 2015).…”