Whole genome sequence of the soybean aphid, Aphis glycines. (August 2020)

• Record Type: Journal Article
• Authors: Wenger, Jacob A.; Cassone, Bryan J.; Legeai, Fabrice; Johnston, J. Spencer; Bansal, Raman; Yates, Ashley D.; Coates, Brad S.; Pavinato, Vitor A.C.; Michel, Andy
• Is Part Of: Insect biochemistry and molecular biology. Volume 123(2020)
• Publication Date: 2020-08
• Subjects: Whole genome -- Aphids -- Aphis glycines -- Genomics; Insect biochemistry -- Periodicals; Insects -- Physiology -- Periodicals; Insects -- Molecular aspects -- Periodicals; Biochemistry -- Periodicals; Insectes -- Biochimie -- Périodiques; Insectes -- Composition -- Périodiques; Insectes -- Physiologie -- Périodiques; Insectes -- Aspect moléculaire -- Périodiques; Biochimie -- Périodiques; Biochemistry; Insect biochemistry; Insects -- Molecular aspects; Insects -- Physiology; Periodicals; 572.8157
• DOI: 10.1016/j.ibmb.2017.01.005
• Languages: English
• ISSNs: 0965-1748

Abstract

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 N50 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. Graphical abstract: Image 1 Highlights: A draft whole genome sequence for Aphis glycines (the soybean aphid) represents the 3rd published aphid genome. The draft genome (302 Mb), combined with flow cytometry (317 Mb), suggest Ap. glycines is the smallest aphid genome to date. Reductions in gene numbers are seen compared to Ac. pisum, possibly related to lack of TE activity and/or specialization.