Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest

Soybean aphid research community

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6 Scopus citations

Abstract

The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number of these duplicated genes. An Illumina GoldenGate assay of 2380 SNPs was used to determine the world-wide population structure of Ap. Glycines. China and South Korean aphids are the closest to those in North America. China is the likely origin of other Asian aphid populations. The most distantly related aphids to those in North America are from Australia. The diversity of Ap. glycines in North America has decreased over time since its arrival. The genetic diversity of Ap. glycines North American population sampled shortly after its first detection in 2001 up to 2012 does not appear to correlate with geography. However, aphids collected on soybean Rag experimental varieties in Minnesota (MN), Iowa (IA), and Wisconsin (WI), closer to high density Rhamnus cathartica stands, appear to have higher capacity to colonize resistant soybean plants than aphids sampled in Ohio (OH), North Dakota (ND), and South Dakota (SD). Samples from the former states have SNP alleles with high FST values and frequencies, that overlap with genes involved in iron metabolism, a crucial metabolic pathway that may be affected by the Rag-associated soybean plant response. The Ap. glycines Biotype 1 genome will provide needed information for future analyses of mechanisms of aphid virulence and pesticide resistance as well as facilitate comparative analyses between aphids with differing natural history and host plant range.

Original languageEnglish (US)
Article number103334
JournalInsect Biochemistry and Molecular Biology
Volume120
DOIs
StatePublished - May 2020

Bibliographical note

Funding Information:
We thank Rosa Alfaro for growing soybean plants. Alvaro G. Hernandez, Chris L. Wright and the staff at the DNA Services Lab, Roy J. Carver Biotechnology Center, University of Illinois at Urbana Champaign, for their excellent sequencing support. Clark W. Bailey, Robert C. Bellm, Scott Berolo, Julie Breault, Hugh Brier, Robert G. Fottit, Dana Gagnier, John Gavloski, Mary Gebhardt, Daniel Guyot, Ronald B. Hammond, Ames Herbert, David Hogg, Doug Johnson, T. Kikuchi, Masafumi Kobayashi, Christian H. Krupke, Brian Lang, Eric L. Maw, Michael McCarville, Andy Michel, Robin Mittenthal, Tamotsu Murai, James Nardi, G. Quesnel, David W. Ragsdale, Tiana Schuster, J.F. Stimmel, Takashi Shigeru, Denis Tagu, Helen Thompson, and Sarah Wilson for assistance in obtaining aphid specimens. Peter D'Eustachio, Joseph Lachance, and John Novembre for comments on theanalysis. Adam Morris from SAS for statistical support. Rebekah D. Wallace, Center of Invasive Species and Ecosystem Health, University of Georgia for help with R. cathartica map. This work was supported by generous grants from the U.S. Mid-West farmers through the checkoff program funds from the United Soybean Board (USB), Illinois Soybean Association (ISA), and the North Central Soybean Research Program (NCSRP) to R. Giordano. Funding was also provided by USDA, Agricultural Research Service, Integrated Management of Soybean Pathogens and Pests, Accession number 432114 to G. L. Hartman, and USDA NIFA grant 2018-67015-28199 to A. V. Zimin. This work is dedicated to the memory of Dr. Richard E. Joost who believed that basic research was essential to the advancement of agriculture and whose support made this work possible.

Funding Information:
This work was supported by generous grants from the U.S. Mid-West farmers through the checkoff program funds from the United Soybean Board (USB), Illinois Soybean Association (ISA), and the North Central Soybean Research Program (NCSRP) to R. Giordano. Funding was also provided by USDA, Agricultural Research Service , Integrated Management of Soybean Pathogens and Pests , Accession number 432114 to G. L. Hartman, and USDA NIFA grant 2018-67015-28199 to A. V. Zimin. This work is dedicated to the memory of Dr. Richard E. Joost who believed that basic research was essential to the advancement of agriculture and whose support made this work possible.

Publisher Copyright:
© 2020 Elsevier Ltd

Keywords

  • Aphid
  • Aphis glycines
  • Biotype 1
  • Genome
  • Phylome
  • Population genetics
  • SNP

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

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