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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 individuals 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 P. nobilis, Pinna rudis and P. nobilis × P. rudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite H. pinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared with that of endosomal TLRs. However, the endosomal TLR‐7 exhibited unexpected level of diversity and haplotype phylogeny. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio, was interpreted as balancing selection, though both directional and purifying selection were detected. Interestingly, roughly 40% of the P. nobilis identified as resistant to H. pinnae were introgressed with P. rudis TLR. Specifically, they all carried a TLR‐7 of P. rudis origin, whereas sensitive P. nobilis were not introgressed, at least at TLR loci. Small contributions of TLR‐6 and TLR‐4 single‐nucleotide polymorphisms to the clustering of resistant and susceptible individuals could be detected, but their specific role in resistance remains highly speculative. This study provides new information on the diversity of TLR genes within the P. nobilis species after MME and additional insights into adaptation to H. pinnae that should contribute to the conservation of this Mediterranean endemic species. [ABSTRACT FROM AUTHOR]

The noble pen shell Pinna nobilis is a Mediterranean endemic and emblematic giant bivalve. Already considered by the late 20th century to be an endangered species, it is facing a dramatic and rapidly expanding epizooty that has decimated populations since mid-2016. The ecological importance of P. nobilis has prompted important investigations for conservation purposes. Here, we report a first analysis of the whole genome sequencing of this animal. This was performed on an Illumina HiSeq X platform using a single paired-end library of short fragments (2 × 150 bp). The de novo contig assembly had a total size of 584 Mb (96,738 contigs, N50 = 7.6 kb, with 0.4% of ambiguous nucleotides), representing 77.5% of the predicted genome size of 754 Mb. The P. nobilis genome is highly AT-rich, with a GC content of 35.6%. At 1%, heterozygosity was in the range of other bivalves with sequenced genomes. Over one-third (36.2%) of the genome consisted of repeated elements with a surprising larger number of short interspersed nuclear elements compared to other molluscan genomes. We were also able to reconstruct the full mitochondrial genome (c. 19 kb, with 12 protein-coding genes, 2 rRNA and 22 tRNA genes). In the context of the epizootic outbreak affecting P. nobilis , a first insight into the innate immune and stress-related genes found in the sequence is provided. [ABSTRACT FROM AUTHOR]