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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 2, 1, * 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 13 Andrew Aschwanden 19 Arian Avalos 18 Mark Band 13 Bryony Bonning 18 Anthony Bretaudeau 20 Olga Chiesa 21 Anitha Chirumamilla 22 Brad Coates 23 Giuseppe Cocuzza 24 Eileen Cullen 25 Peter Desborough 26 Brian Diers 13 Christina Difonzo 27 George Heimpel 28 Theresa Herman 13 Yongping Huanga 29 Janet Knodel 22 Chiun-Cheng Ko 30 Genevieve Labrie 31 Doris Lagos-Kutz 32 Joon-Ho Lee 33 Seunghwan Lee 33 Fabrice Legeai 20, 34 Mauro Mandrioli 35 Gian Carlo Manicardi 36 Emanuele Mazzoni 37 Giulia Melchiori 36 Ana Micijevic 38 Nick Miller 39 Andi Nasuddin 40 Brian Nault 41 Matthew O'Neal 23 Michela Panini 18 Massimo Pessino 13 Deirdre Prischmann-Voldseth 22 Hugh Robertson 13 Hojun Song 23 Kelley Tilmon 42 John Tooker 43 Kongming Wu 44 Shuai Zhan 44
* Corresponding author
34 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
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 : Tuesday, January 4, 2022 - 6:34:13 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.1-24. ⟨10.1016/j.ibmb.2020.103334⟩. ⟨hal-03065382⟩

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