Background The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. Results Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis , with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. Conclusions Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.

中文翻译：

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地中海贻贝中巨大的基因存在与缺失变异塑造了开放的泛基因组


背景地中海贻贝（Mytilus galloprovincialis）是一种具有生态和经济意义的可食用海洋双壳类动物，具有高度侵入性，对生物和非生物应激源具有很强的抵抗力，导致其他双壳类动物反复出现大规模死亡。尽管这些特征最近与自然种群内高遗传变异的维持有关，但该物种进化成功的潜在因素仍不清楚。结果在这里，在组装了 1.28 Gb 参考基因组并对来自两个独立种群的 14 个个体进行重新测序后，我们揭示了 M. galloprovincialis 复杂的泛基因组结构，其中包含 45,000 个核心基因组以及数量惊人的基因组。可有可无的基因（20,000）受到存在与不存在变异的影响，这些基因可能在几个个体中完全缺失。我们表明，可有可无的基因与受结构变异影响的半合子基因组区域相关，这些区域总共占近 580 Mb 的 DNA 序列，未包含在参考基因组组装中。因此，这是第一项报告动物界全基因组范围内基因存在与缺失变异广泛发生的研究。结论 可有可无的基因通常属于年轻的、最近扩展的、富含生存功能的基因家族，这可能是解释该物种的恢复力和入侵性的关键。这种独特的泛基因组结构的特点是辅助基因组区域中的可有可无的基因超出了在包括人类在内的其他后生动物中观察到的数量级，并且密切反映了原核生物和一些非后生动物真核生物中发现的开放泛基因组。