The king scallop, Pecten maximus is a well-known, commercially important scallop species and is featured with remarkable tolerance to potent phytotoxins such as domoic acid. A high-quality genome can shed light on its biology and innovative evolution of toxin resistance. A reference genome has recently been generated for P. maximus, however, it is suspicious that over 67,700 genes are annotated in this genome, which is unexpectedly larger than its close relatives of pectinids. Herein, we provide an improved high-quality chromosome-level reference genome sequence for the king scallop P. maximus. A final set of 26,995 genes is annotated after carefully checking and curation of the predicted gene models, which significantly improves the accuracy of gene structure information. The large number of gene duplicates in the previous genome is mainly distorted by the fragmented annotation. Through integrated genomic, evolutionary and transcriptomic analyses, we reveal that the Phi subfamily of ionotropic glutamate receptors (iGluRs) are well preserved in molluscs, and P. maximus experienced the rapid expansion of the Phi class of iGluR (GluF) gene family. The GluF genes exhibit ubiquitously high expression and altered sequence characteristics for ligand selectivity, which may contribute to the remarkable tolerance to neurotoxins in P. maximus. Taken together, our study disapproves the previous claim of the 'gene-rich' genome of this species and provides a high-quality genome assembly for further understanding of its biology and evolution of toxin-resistance.

扇贝王 ( Pecten maximus)是一种著名的、具有重要商业价值的扇贝品种，具有对软骨藻酸等强效植物毒素具有显着耐受性的特点。高质量的基因组可以揭示其生物学和毒素抗性的创新进化。最近已经为P. maximus生成了一个参考基因组，然而，令人怀疑的是，该基因组中注释了超过 67,700 个基因，其出乎意料地大于其近亲果胶类。在此，我们为扇贝大扇贝提供了改进的高质量染色体水平参考基因组序列。经过仔细检查和整理预测的基因模型后，最终对 26,995 个基因进行了注释，这显着提高了基因结构信息的准确性。先前基因组中大量的基因重复主要是由于片段化的注释而扭曲的。通过综合基因组、进化和转录组分析，我们揭示了离子型谷氨酸受体（iGluR）的Phi亚家族在软体动物中得到了很好的保存，并且大对虾经历了iGluR（GluF）基因家族的Phi类的快速扩张。GluF 基因表现出普遍的高表达和配体选择性的改变的序列特征，这可能有助于大虾对神经毒素的显着耐受性。综上所述，我们的研究否定了之前关于该物种基因组“基因丰富”的说法，并提供了高质量的基因组组装，以进一步了解其生物学和抗毒素进化。