Abstract
Woolly apple aphid (WAA, Eriosoma lanigerum Hausmann) (Hemiptera: Aphididae) is a major pest of apple trees (Malus domestica, order Rosales) and is critical to the economics of the apple industry in most parts of the world. Here, we generated a chromosome-level genome assembly of WAA-representing the first genome sequence from the aphid subfamily Eriosomatinae-using a combination of 10X Genomics linked-reads and in vivo Hi-C data. The final genome assembly is 327Mb, with 91% of the assembled sequences anchored into six chromosomes. The contig and scaffold N50 values are 158kb and 71Mb, respectively, and we predicted a total of 28,186 protein-coding genes. The assembly is highly complete, including 97% of conserved arthropod single-copy orthologues based on Benchmarking Universal Single-Copy Orthologs (busco) analysis. Phylogenomic analysis of WAA and nine previously published aphid genomes, spanning four aphid tribes and three subfamilies, reveals that the tribe Eriosomatini (represented by WAA) is recovered as a sister group to Aphidini+Macrosiphini (subfamily Aphidinae). We identified syntenic blocks of genes between our WAA assembly and the genomes of other aphid species and find that two WAA chromosomes (El5 and El6) map to the conserved Macrosiphini and Aphidini X chromosome. Our high-quality WAA genome assembly and annotation provides a valuable resource for research in a broad range of areas such as comparative and population genomics, insect-plant interactions and pest resistance management.
Highlights
There are approximately 5,000 known species of aphid (Hemiptera: Aphididae), and approximately 100 of these are of significant agricultural economic importance (Blackman & Eastop, 2017)
It was likely introduced to Britain in 1796 or 1797 with infested apple trees imported from America (Theobald, 1920) and has subsequently become a cosmopolitan and highly-damaging pest of apple worldwide (Barbagallo et al, 1997)
Before running the gene prediction, we identified repeats and transposable elements (TEs) with RepeatMasker v4.0.7 (Tarailo-Graovac & Chen, 2009) using the RepBase Insecta repeat library (Bao, Kojima, & Kohany, 2015) with the parameters “-e ncbi -species insecta -a -xsmall -gff” (Jurka et al, 2005)
Summary
There are approximately 5,000 known species of aphid (Hemiptera: Aphididae), and approximately 100 of these are of significant agricultural economic importance (Blackman & Eastop, 2017). This report represents the first complete genome sequence for a species from the Eriosomatinae subfamily which includes three potentially polyphyletic tribes (Eriosomatini, Fordini and Pemphigini), all of which are distantly related to members of Aphidinae Edaphic (soil-dwelling) WAA has a significant negative effect on plant growth, especially of young, non-bearing apple trees where feeding significantly reduces trunk diameter (Brown, Schmitt, Ranger, & Hogmire, 1995) that is strongly correlated with fruit production (Waring, 1920). Such widespread and significant damage has made WAA resistance a key objective for rootstock breeding since the early 20th century (Cummins & Aldwinckle, 1983)
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