First insight into the whole genome shotgun sequence of the endangered noble pen shell Pinna nobilis: a giant bivalve undergoing a mass mortality event

Abstract

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.