Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK.
BMC Genomics. 2022 Mar 12;23(1):198. doi: 10.1186/s12864-022-08436-5.
Sphaerophoria rueppellii, a European species of hoverfly, is a highly effective beneficial predator of hemipteran crop pests including aphids, thrips and coleopteran/lepidopteran larvae in integrated pest management (IPM) programmes. It is also a key pollinator of a wide variety of important agricultural crops. No genomic information is currently available for S. rueppellii. Without genomic information for such beneficial predator species, we are unable to perform comparative analyses of insecticide target-sites and genes encoding metabolic enzymes potentially responsible for insecticide resistance, between crop pests and their predators. These metabolic mechanisms include several gene families - cytochrome P450 monooxygenases (P450s), ATP binding cassette transporters (ABCs), glutathione-S-transferases (GSTs), UDP-glycosyltransferases (UGTs) and carboxyl/choline esterases (CCEs).
In this study, a high-quality near-chromosome level de novo genome assembly (as well as a mitochondrial genome assembly) for S. rueppellii has been generated using a hybrid approach with PacBio long-read and Illumina short-read data, followed by super scaffolding using Hi-C data. The final assembly achieved a scaffold N50 of 87Mb, a total genome size of 537.6Mb and a level of completeness of 96% using a set of 1,658 core insect genes present as full-length genes. The assembly was annotated with 14,249 protein-coding genes. Comparative analysis revealed gene expansions of CYP6Zx P450s, epsilon-class GSTs, dietary CCEs and multiple UGT families (UGT37/302/308/430/431). Conversely, ABCs, delta-class GSTs and non-CYP6Zx P450s showed limited expansion. Differences were seen in the distributions of resistance-associated gene families across subfamilies between S. rueppellii and some hemipteran crop pests. Additionally, S. rueppellii had larger numbers of detoxification genes than other pollinator species.
This assembly is the first published genome for a predatory member of the Syrphidae family and will serve as a useful resource for further research into selectivity and potential tolerance of insecticides by beneficial predators. Furthermore, the expansion of some gene families often linked to insecticide resistance and selectivity may be an indicator of the capacity of this predator to detoxify IPM selective insecticides. These findings could be exploited by targeted insecticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably and effectively controlling pests without impacting beneficial predator populations.
欧洲食蚜虻属的捕食性蝇类，是一种高效的有益捕食者，在综合虫害管理（IPM）计划中捕食包括蚜虫、蓟马和鞘翅目/鳞翅目幼虫在内的半翅目作物害虫。它也是多种重要农业作物的关键传粉媒介。目前还没有关于 Sphaerophoria rueppellii 的基因组信息。如果没有这些有益捕食者物种的基因组信息，我们就无法对作物害虫及其捕食者之间的杀虫剂靶标和代谢酶基因进行比较分析，这些代谢酶基因可能与杀虫剂抗性有关。这些代谢机制包括几个基因家族 - 细胞色素 P450 单加氧酶（P450s）、ATP 结合盒转运蛋白（ABCs）、谷胱甘肽-S-转移酶（GSTs）、UDP-糖基转移酶（UGTs）和羧酸/胆碱酯酶（CCEs）。
在这项研究中，使用 PacBio 长读长和 Illumina 短读长数据的混合方法，以及使用 Hi-C 数据进行超级支架，生成了 Sphaerophoria rueppellii 的高质量近染色体水平从头基因组组装（以及线粒体基因组组装）。最终组装的支架 N50 为 87Mb，基因组大小为 537.6Mb，使用一套全长基因的 1658 个核心昆虫基因，完整性达到 96%。该组装使用 14249 个蛋白编码基因进行注释。比较分析表明，CYP6Zx P450s、epsilon 类 GSTs、膳食 CCEs 和多个 UGT 家族（UGT37/302/308/430/431）发生了基因扩张。相反，ABCs、delta 类 GSTs 和非 CYP6Zx P450s 的扩张有限。在 Sphaerophoria rueppellii 和一些半翅目作物害虫之间，抗性相关基因家族在亚家族中的分布存在差异。此外，Sphaerophoria rueppellii 比其他传粉媒介物种拥有更多的解毒基因。
该组装是食蚜蝇科捕食性成员的第一个已发表基因组，将成为进一步研究有益捕食者对杀虫剂的选择性和潜在耐受性的有用资源。此外，一些与杀虫剂抗性和选择性经常相关的基因家族的扩张可能是该捕食者解毒 IPM 选择性杀虫剂能力的一个指标。这些发现可以通过有针对性的杀虫剂筛选和功能研究来利用，以提高 IPM 策略的有效性，从而通过可持续和有效地控制害虫来增加作物产量，而不影响有益捕食者的数量。
