Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae)

Abstract

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, A. piceae, A. laricis, Pineus pini, and P. 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-seq 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 Mb and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and 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, three publicly available adelgid transcriptomes, four phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, four aphid genomes, and two 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 non-coding 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.

Phylloxera and Aphids Show Distinct Features of Genome Evolution Despite Similar Reproductive Modes

“…To determine whether the difference between autosomes and X chromosome extends to phylloxera, we separately compared aphids and phylloxera with Adelges cooleyi , a member of the family Adelgidae, a third related lineage undergoing cyclical parthenogenesis. The A. cooleyi genome was recently sequenced, along with phylogenetic analyses strongly supporting adelgids and phylloxera as sister groups within Aphidomorpha ( Dial et al 2023 ). Thus, if parthenogenesis is responsible for autosomal rearrangements, the elevated autosomal rearrangements should be present in both comparisons.…”

Effective population size of X chromosomes and haplodiploids under cyclical parthenogenesis

“…From these results we should always expect less diversity on the X chromosomes than the autosomes, and with the most pronounced differences in those populations with frequent sexual reproduction. Aphids may provide good systems to test this hypothesis, and there are an increasing number of aphid species (and close relatives) which now have chromosome level genome assemblies (Mathers et al 2021; Dial et al 2023; Li et al 2023). Most aphids must reproduce sexually to produce overwintering eggs, but the number of possible asexual generations scales with the length of the breeding season (Simon et al 2002).…”