Genome sequencing and assembly of Aphelinus atriplicis and Aphelinus certus

Safe, effective biological-control introductions against invasive pests depend on narrowly host-specific natural enemies with the ability to adapt to a changing environment. As part of a project on the genetic architectures of these traits, we assembled and annotated the genomes of two aphid parasitoids, Aphelinus atriplicis and Aphelinus certus. We report here several assemblies made using Illumina and PacBio data, which we combined into a meta-assembly. We scaffolded the meta-assembly with markers from a genetic map of hybrids between A. atriplicis and A. certus. We used this genetic-linkage scaffolded (GLS) assembly of A. atriplicis to scaffold a de novo assembly of A. certus. The de novo assemblies differed in contiguity, and the meta-assembly was more contiguous than the best de novo assembly. Scaffolding with genetic-linkage data allowed chromosomal-level assembly of the A. atriplicis genome, and scaffolding a de novo assembly of A. certus with this GLS assembly, greatly increased the contiguity of the A. certus assembly. However, completeness of the A. atriplicis assembly, as measured by percent of the complete, single-copy BUSCO hymenopteran genes, varied little among de novo assemblies and was not increased by meta-assembly or genetic scaffolding. Furthermore, the greater contiguity of the meta-assembly and GLS assembly had little or no effect on the numbers of genes identified, the proportion with homologs or functional annotations. Increased contiguity of the A. certus assembly provided modest improvement in assembly completeness, as measured by the percent complete, single-copy BUSCO hymenopteran genes. The total genic sequence increased, and while the number of genes declined, gene length increased, which together suggests greater accuracy of gene models. More contiguous assemblies provide uses other than gene annotation, for example, identifying the genes associated with quantitative trait loci and understanding of chromosomal rearrangements associated with speciation.

安全有效的生物防治入侵害虫依赖于具有适应环境变化能力的、对宿主选择狭窄的自然天敌。在探讨此类性状遗传结构的项目中，我们收集并注释了两种蚜虫寄生蜂——Aphelinus atriplicis 和 Aphelinus certus 的基因组。在此，我们报告了利用 Illumina 和 PacBio 数据构建的数个组装，并将它们合并为一个元组装。我们利用 A. atriplicis 和 A. certus 杂交种系的遗传图谱中的标记对元组装进行了支架构建。利用此遗传连锁支架（GLS）组装的 A. atriplicis 对 A. certus 的从头组装进行了支架构建。从头组装在连续性上存在差异，元组装的连续性优于最佳从头组装。利用遗传连锁数据进行的支架构建实现了 A. atriplicis 基因组的染色体级组装，并且使用该 GLS 组装对 A. certus 的从头组装进行支架构建，显著提高了 A. certus 组装的连续性。然而，以完整、单拷贝 BUSCO hymenopteran 基因的百分比衡量的 A. atriplicis 组装的完整性变化不大，元组装或遗传支架构建并未增加其完整性。此外，元组装和 GLS 组装的更高连续性对基因识别数量、同源或功能注释的比例影响甚微或无影响。A. certus 组装的连续性提高为组装完整性提供了适度的改进，以完整、单拷贝 BUSCO hymenopteran 基因的百分比衡量。总基因序列增加，尽管基因数量减少，但基因长度增加，这共同表明基因模型准确性更高。更连续的组装除了基因注释之外，还有其他用途，例如识别与数量性状位点相关的基因，以及理解与物种形成相关的染色体重排。