Genome description and inventory of immune-related genes of the endangered pen shell Pinna nobilis: a giant bivalve experiencing a mass mortality event

Abstract

Background: The noble pen shell Pinna nobilis is a Mediterranean endemic and emblematic giant bivalve. Already registered as an endangered species in the late 20th century, it is facing a dramatic and rapidly expanding epizooty that decimates its populations since mid-2016. The ecological value of P. nobilis has urged important investigations for conservation purposes. In light of this, we report here the first draft genome of this animal. Results: The whole-genome sequencing has been performed on an Illumina HiSeq X platform using a single paired-end library of short fragments (2x150 bp). The de novo contig assembly accounted for a total size of 584 Mb (96,738 contigs, N50 = 7.6 kb, with 0.4% of “N” nucleotides), representing 77.5% of the predicted genome size of 754 Mb. The pen shell genome is very AT-rich, with a GC-content of 35.6 %. Heterozygosity was found to be in the range of other sequenced bivalves (1%). Over one third (36.2 %) of the genome consisted of repeated elements with a surprising larger number of SINEs elements compared to other molluscan genomes. We were also able to reconstruct the full mitochondrial genome (~19 kb, with 12 protein-coding genes, 2 rRNA and 22 tRNA genes). In relation with the outbreak that affects P. nobilis, we paid a special attention on the innate immune and stress-related genes found in the sequence. We revealed that P. nobilis disposes of a complete chemical defensome, and a relatively sophisticated innate immune system. Conclusion: In addition to offering a valuable resource for further research in comparative biology and evolution, access to the draft genome sequence is central to deepen our understanding of the vulnerability of P. nobilis to new diseases, which are likely to occur more often in the current scenario of a rapidly changing environment.

Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis

“…Both TLRs and PGRPs have been suggested to participate in endosymbiont establishment and symbiosis regulation ( Li et al, 2021 ; Sun et al, 2017 ). TLRs and PGRPs also function in pathogenic infection, with the latter able to induce phagocytosis ( Bunet et al, 2019 ). Thus, they may also play a role in the recognition and response of epibiotic Campylobacteria.…”