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.

中文翻译：

---

首次深入了解濒临灭绝的贵族钢笔壳 Pinna nobilis 的全基因组鸟枪序列：一种正在经历大规模死亡事件的巨型双壳类动物

高贵的笔壳 Pinna nobilis 是地中海特有的标志性巨型双壳类动物。到 20 世纪后期已被视为濒临灭绝的物种，它正面临着一场剧烈且迅速扩大的流行病，自 2016 年年中以来，该流行病的种群数量已大幅减少。P. nobilis 的生态重要性促使人们出于保护目的进行重要调查。在这里，我们报告了对这种动物全基因组测序的首次分析。这是在 Illumina HiSeq X 平台上使用短片段（2 × 150 bp）的单个配对末端文库进行的。从头 contig 组装的总大小为 584 Mb（96,738 个 contig，N50 = 7.6 kb，含 0.4% 的不明确核苷酸），占预测的 754 Mb 基因组大小的 77.5%。P. nobilis 基因组高度富含 AT，GC 含量为 35.6%。在 1% 时，杂合性在其他基因组测序的双壳类动物的范围内。与其他软体动物基因组相比，超过三分之一 (36.2%) 的基因组由重复元素组成，其中短散布的核元素数量惊人地多。我们还能够重建完整的线粒体基因组（约 19 kb，具有 12 个蛋白质编码基因、2 个 rRNA 和 22 个 tRNA 基因）。在影响 P. nobilis 的动物流行病爆发的背景下，提供了对序列中发现的先天免疫和压力相关基因的第一次洞察。具有 12 个蛋白质编码基因、2 个 rRNA 和 22 个 tRNA 基因）。在影响 P. nobilis 的动物流行病爆发的背景下，提供了对序列中发现的先天免疫和压力相关基因的第一次洞察。具有 12 个蛋白质编码基因、2 个 rRNA 和 22 个 tRNA 基因）。在影响 P. nobilis 的动物流行病爆发的背景下，提供了对序列中发现的先天免疫和压力相关基因的第一次洞察。