The fan mussel Pinna nobilis is currently on the brink of extinction due
to a multifactorial disease mainly caused to the highly pathogenic
parasite Haplosporidium pinnae, meaning that the selection pressure
outweighs the adaptive potential of the species. Hopefully, rare
specimens have been observed somehow resistant to the parasite,
stretching the need to identify the traits underlying this better
fitness. Among the candidate to explore at first intention are fast
evolving immune genes, of which toll-like receptor (TLR). In this study,
we examined the genetic diversity at 14 TLR loci across Pinna nobilis,
Pinna rudis and Pinna nobilis x Pinna rudis hybrid genomes, collected at
four physically distant regions, that were found to be either resistant
or sensitive to the parasite Haplosporidium pinnae. We report a high
genetic diversity, mainly observed at cell surface TLRs compared to that
of endosomal TLRs. However, the TLR-7 and TLR-1 exhibited unexpected
level of diversity and haplotype phylogeny, respectively. The lack of
population structure, associated with a high genetic diversity and
elevated dN/dS ratio were interpreted as balancing selection, though
both directional and purifying selection were detected. Overall, we
observed small contributions of putatively selected SNPs involved in the
resistance. However, the most contributing SNPs were carried by two
TLR-6 loci and might be used as potent biomarkers of distinguish between
resistant and sensitive P. nobilis individuals. Moreover, more than 10%
of P. nobilis individuals were found introgressed with P. rudis.
Noteworthy, all introgressed P. nobilis observed as resistant to H.
pinnae carried a TLR-7 of P. rudis origin. This study contributes to the
ongoing efforts towards conservation carried out to prevent from
extinction this Mediterranean endemic species.