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

Rosanna Giordano 1, 2, * Ravi Kiran Donthu 3, 2, * Aleksey Zimin 3 Irene Consuelo Julca Chavez 4, 5, 6 Toni Gabaldon 6, 4, 5, 7 Manuella van Munster 8 Lawrence Hon 9 Richard Hall 10 Jonathan Badger 11 Minh Nguyen 12 Alejandra Flores 13 Bruce Potter 14 Tugrul Giray 15 Felipe Soto-Adames 16 Everett Weber 2 Jose Marcelino 2, 1, 16 Christopher Fields 13 David Voegtlin 13 Curt Hill 17 Glen Hartman 13, 18 Tatsiana Akraiko Andrew Aschwanden Arian Avalos Mark Band Bryony Bonning Anthony Bretaudeau Olga Chiesa Anitha Chirumamilla Brad Coates Giuseppe Cocuzza Eileen Cullen Peter Desborough Brian Diers Christina Difonzo George Heimpel Theresa Herman Yongping Huanga Janet Knodel Chiun-Cheng Ko Genevieve Labrie Doris Lagos-Kutz Joon-Ho Lee Seunghwan Lee Fabrice Legeai 19, 20 Mauro Mandrioli Gian Carlo Manicardi Emanuele Mazzoni Giulia Melchiori Ana Micijevic Nick Miller Andi Nasuddin Brian Nault Matthew O'Neal Michela Panini Massimo Pessino Deirdre Prischmann-Voldseth Hugh Robertson Hojun Song Kelley Tilmon John Tooker Kongming Wu Shuai Zhan
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.
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https://hal.inria.fr/hal-03065382
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Submitted on : Monday, December 14, 2020 - 6:20:23 PM
Last modification on : Wednesday, January 20, 2021 - 10:18:02 AM

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Rosanna Giordano, Ravi Kiran Donthu, Aleksey Zimin, Irene Consuelo Julca Chavez, Toni Gabaldon, et al.. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. Insect Biochemistry and Molecular Biology, Elsevier, 2020, 120, pp.103334. ⟨10.1016/j.ibmb.2020.103334⟩. ⟨hal-03065382⟩

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