Aphidius gifuensis is a parasitoid wasp that has been commercially bred and released in large scale as a biocontrol agent for the management of aphid pests. As a highly efficient endoparasitoid, it is also an important model for exploring mechanisms of parasitism. Currently, artificially bred populations of this wasp are facing rapid decline with undetermined cause, and mechanisms underlying its parasitoid strategy remain poorly understood. Exploring the mechanism behind its population decline and the host–parasitoid relationship is impeded partly due to the lack of a comprehensive genome data for this species. In this study, we constructed a high‐quality reference genome of A. gifuensis using Oxford Nanopore sequencing and Hi‐C (proximity ligation chromatin conformation capture) technology. The final genomic assembly was 156.9 Mb, with a contig N50 length of 3.93 Mb, the longest contig length of 10.4 Mb and 28.89% repetitive sequences. 99.8% of genome sequences were anchored onto six linkage groups. A total of 11,535 genes were predicted, of which 90.53% were functionally annotated. Benchmarking Universal Single‐Copy Orthologs (BUSCO) analysis showed the completeness of assembled genome is 98.3%. We found significantly expanded gene families involved in metabolic processes, transmembrane transport, cell signal communication and oxidoreductase activity, in particular ATP‐binding cassette (ABC) transporter, Cytochrome P450 and venom proteins. The olfactory receptors (ORs) showed significant contraction, which may be associated with the decrease in host recognition. Our study provides a solid foundation for future studies on the molecular mechanisms of population decline as well as host–parasitoid relationship for parasitoid wasps.

中文翻译：

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使用牛津纳米孔测序和 Hi-C 技术的蚜虫寄生蜂 Aphidius gifuensis 的染色体水平基因组组装

Aphidius gifuensis是一种寄生蜂，已被商业培育并大规模释放，作为管理蚜虫害虫的生物防治剂。作为一种高效的内寄生生物，它也是探索寄生机制的重要模型。目前，这种黄蜂的人工繁殖种群正面临不明原因的快速下降，其寄生策略的潜在机制仍知之甚少。由于缺乏该物种的全面基因组数据，探索其种群下降和寄主-寄生物关系背后的机制受到阻碍。在这项研究中，我们构建了一个高质量的A. gifuensis参考基因组使用牛津纳米孔测序和 Hi-C（邻近连接染色质构象捕获）技术。最终的基因组组装为 156.9 Mb，contig N50 长度为 3.93 Mb，最长的 contig 长度为 10.4 Mb，重复序列为 28.89%。99.8% 的基因组序列锚定在六个连锁群上。共预测了 11,535 个基因，其中 90.53% 被功能注释。基准通用单拷贝直向同源物 (BUSCO) 分析显示组装基因组的完整性为 98.3%。我们发现参与代谢过程、跨膜转运、细胞信号通讯和氧化还原酶活性的基因家族显着扩大，特别是 ATP 结合盒 (ABC) 转运蛋白、细胞色素 P450 和毒液蛋白。嗅觉受体（ORs）显着收缩，这可能与宿主识别的减少有关。我们的研究为未来研究寄生蜂种群下降的分子机制以及寄主-寄生蜂关系提供了坚实的基础。