Department of Entomology, University of Georgia, Athens, GA 30602, USA.
Department of Biology, Utah State University, Logan, UT 84322, USA.
G3 (Bethesda). 2023 Dec 29;14(1). doi: 10.1093/g3journal/jkad224.
The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.
球蚜科（Adelgidae）是一类吸食汁液的小昆虫，与真正的蚜虫（Aphididae）和叶蝉科（Phylloxeridae）一起构成了蚜总科（Aphidomorpha）。一些球蚜物种对森林生态系统具有高度破坏性，如白松球蚜（Adelges tsugae）、云杉球蚜（Adelges piceae）、落叶松球蚜（Adelges laricis）、松针长足大蚜（Pinus pini）和松针长足小蚜（Pineus boerneri）。尽管如此，球蚜科内和蚜总科内的高级基因组分析仍然缺乏高质量的基因组资源。在这里，我们使用 PacBio 连续长读和 Illumina RNA 测序技术，为北美特有种 Cooley 云杉瘿球蚜（Adelges cooleyi（Gillette））构建了高质量的基因组草图。组装的基因组总大小为 270.2 Mb，支架和 contig N50 分别为 14.87 和 7.18 Mb。共预测到 24967 个编码序列，用 Arthropoda 和 Hemiptera 的核心 BUSCO 基因集估计组装的完整性分别为 98.1%和 99.6%。基于 A. cooleyi 基因组、3 个公开的球蚜转录组、4 个叶蝉转录组、Daktulosphaira vitifoliae（葡萄根瘤蚜）基因组、4 个蚜虫基因组和 2 个外群球蚜基因组的系统发育基因组分析，完全解决了球蚜和叶蝉科的系统发育关系，表明它们是姐妹群。线粒体基因组大小为 24 kb，是迄今为止采样的昆虫中最大的之一，其中 39.4%由非编码区组成。这个基因组组装是目前唯一的球蚜科基因组规模的注释组装，将成为理解蚜总科的生态学和进化的有价值的资源。
