Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA.
Ecology and Genetics of Insects & INRIA/IRISA, Genscale, Campus Beaulieu, Rennes, INRA, UMR IGEPP 1349, France.
Insect Biochem Mol Biol. 2020 Aug;123:102917. doi: 10.1016/j.ibmb.2017.01.005. Epub 2017 Jan 22.
Aphids are emerging as model organisms for both basic and applied research. Of the 5,000 estimated species, only three aphids have published whole genome sequences: the pea aphid Acyrthosiphon pisum, the Russian wheat aphid, Diuraphis noxia, and the green peach aphid, Myzus persicae. We present the whole genome sequence of a fourth aphid, the soybean aphid (Aphis glycines), which is an extreme specialist and an important invasive pest of soybean (Glycine max). The availability of genomic resources is important to establish effective and sustainable pest control, as well as to expand our understanding of aphid evolution. We generated a 302.9 Mbp draft genome assembly for Ap. glycines using a hybrid sequencing approach. This assembly shows high completeness with 19,182 predicted genes, 92% of known Ap. glycines transcripts mapping to contigs, and substantial continuity with a scaffold N of 174,505 bp. The assembly represents 95.5% of the predicted genome size of 317.1 Mbp based on flow cytometry. Ap. glycines contains the smallest known aphid genome to date, based on updated genome sizes for 19 aphid species. The repetitive DNA content of the Ap. glycines genome assembly (81.6 Mbp or 26.94% of the 302.9 Mbp assembly) shows a reduction in the number of classified transposable elements compared to Ac. pisum, and likely contributes to the small estimated genome size. We include comparative analyses of gene families related to host-specificity (cytochrome P450's and effectors), which may be important in Ap. glycines evolution. This Ap. glycines draft genome sequence will provide a resource for the study of aphid genome evolution, their interaction with host plants, and candidate genes for novel insect control methods.
蚜虫正在成为基础和应用研究的模式生物。在估计的 5000 个物种中，只有三种蚜虫的全基因组序列已经公布：豌豆蚜 Acyrthosiphon pisum、俄罗斯麦蚜 Diuraphis noxia 和桃蚜 Myzus persicae。我们介绍了第四种蚜虫——大豆蚜（Aphis glycines）的全基因组序列，它是一种极端专化的大豆重要入侵害虫。基因组资源的可用性对于建立有效的和可持续的害虫防治以及扩大我们对蚜虫进化的理解非常重要。我们使用混合测序方法为大豆蚜生成了一个 302.9 Mbp 的基因组草图组装。该组装具有很高的完整性，预测了 19182 个基因，92%的已知大豆蚜转录本映射到 contigs 上，并且与支架 N 的连续性很高，长度为 174505 bp。该组装基于流式细胞术预测的基因组大小 317.1 Mbp 的 95.5%。基于对 19 种蚜虫物种的更新基因组大小，大豆蚜的基因组是迄今为止已知的最小的蚜虫基因组。大豆蚜基因组组装的重复 DNA 含量（81.6 Mbp 或 302.9 Mbp 组装的 26.94%）与豌豆蚜相比，分类转座元件的数量减少，这可能有助于估计基因组较小。我们包括了与宿主特异性相关的基因家族（细胞色素 P450 和效应子）的比较分析，这可能在大豆蚜的进化中很重要。这个大豆蚜的基因组草图序列将为研究蚜虫基因组进化、它们与宿主植物的相互作用以及新型昆虫控制方法的候选基因提供资源。
