The whole genome sequence assembly of the soybean aphid, Aphis glycines

Authors: WENGER, JACOB - The Ohio State University; CASSONE, BRYAN - The Ohio State University; LEGEAI, FABRICE - Institut National De La Recherche Agronomique (INRA); JOHNSTON, SPENCER - Texas A&M University; BANSAL, RAMAN - The Ohio State University; YATES, ASHLEY - The Ohio State University; Coates, Brad; MICHEL, ANDREW - The Ohio State University

Submitted to: Insect Biochemistry and Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/14/2017
Publication Date: 1/22/2017
Citation: Wenger, J.A., Cassone, B.J., Legeai, F., Johnston, S., Bansal, R., Yates, A.D., Coates, B.S., Michel, A. 2017. The whole genome sequence assembly of the soybean aphid, Aphis glycines. Insect Biochemistry and Molecular Biology. doi:10.1016/j.ibmb.2017.01.005.

Interpretive Summary: Soybeans are a major agricultural commodity grown in the United States which serves as an important protein source for animal feedstock and direct human consumption. Damage caused to soybean plants by the soybean aphid result in reduced plant vigor and subsequent yield. Moreover, soybean aphids are capable of transmitting plant viruses that further reduce crop yields and producer profits. Soybean aphids have adapted for survival on soybean varieties that were bred to repel their feeding, and represents an instance where insect adaptations have resulted in resistance to producer control practices. An entire genome sequence assembly was generated by an ARS scientist in collaboration with University collaborators and international partners, from which the sequence and distribution of genes families and transposable element were estimated. The relatively small size of the soybean aphid genome compared to other aphid species appears to result from a small proportion of mobile DNA elements. This genome sequence will be a valuable resource to University, Industry and Government scientists for investigating the genetic mechanisms soybean aphids use to overcome host plant resistance traits.

Technical Abstract: Aphids are emerging as model organisms for both basic and applied research. Of the 5,000 estimated species, only two aphids have published whole genome sequences: the pea aphid Acyrthosiphon pisum, and the Russian wheat aphid, Diuraphis noxia. The soybean aphid (Aphis glycines) is an extreme specialist, as well as 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. A 302.9 Mb draft genome assembly for Ap. glycines was obtained using a hybrid sequencing approach. This assembly shows high completeness with 92% of Ap. glycines transcripts mapping to contigs, and continuity with a contig N50 of 174,505 bp. The assembly represents 95% of the predicted genome size of 319Mb based on flow cytometry and represents the smallest aphid genome to date. The repetitive DNA content of the Ap. glycines genome assembly (81.6 Mbp or 26.94% of the 302.9 Mbp assembly), with a reduction in the number of classified transposable elements compared to the pea aphid, Ap. pisum. A total of 19,182 gene models were predicted via evidence based and ab initio models, of which the diversity of gene families related to host-specificity (cytochrome P450’s and effectors) are described in detail. This Ap. glycines draft genome sequence will provide a resource for the study of aphid genomic evolution and candidate genes for novel insect control methods.