title: Whole genome sequence of the soybean aphid, Aphis glycines.
abstract: 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 N50of 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.
authors.affiliation: 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.
authors.forename: Jacob A
authors.initials: JA
authors.lastname: Wenger
authors.affiliation: 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.
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Cassone
authors.affiliation: Ecology and Genetics of Insects & INRIA/IRISA, Genscale, Campus Beaulieu, Rennes, INRA, UMR IGEPP 1349, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Legeai
authors.affiliation: Department of Entomology, Texas A&M University, College Station, TX, USA.
authors.forename: J Spencer
authors.initials: JS
authors.lastname: Johnston
authors.affiliation: Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA.
authors.forename: Raman
authors.initials: R
authors.lastname: Bansal
authors.affiliation: 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.
authors.forename: Ashley D
authors.initials: AD
authors.lastname: Yates
authors.affiliation: USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, USA.
authors.forename: Brad S
authors.initials: BS
authors.lastname: Coates
authors.affiliation: Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA.
authors.forename: Vitor A C
authors.initials: VAC
authors.lastname: Pavinato
authors.affiliation: 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. Electronic address: michel.70@osu.edu.
authors.forename: Andy
authors.initials: A
authors.lastname: Michel
mesh_terms: D000818:Animals; D001042:Aphids / Q000235:genetics*; D005075:Biological Evolution; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D059646:Genome Size; D049750:Genome, Insect; D023281:Genomics; D010571:Pest Control; D010802:Phylogeny; D013025:Glycine max
chemical_list: D004251:DNA Transposable Elements; D003577:Cytochrome P-450 Enzyme System
keywords: Aphids; Aphis glycines; Genomics; Whole genome