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 A.P. 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)
,
Mauro Mandrioli
(34)
,
Gian Carlo Manicardi
(35)
,
Emanuele Mazzoni
(36)
,
Giulia Melchiori
(35)
,
Ana Micijevic
(37)
,
Nick Miller
(38)
,
Andi Nasuddin
(39)
,
Brian Nault
(40, 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)
1
Puerto Rico Science
2 Know Your Bee Inc
3 JHU - Johns Hopkins University
4 BIST - Barcelona Institute of Science and Technology
5 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
6 CRG-UPF - Center for Genomic Regulation
7 IRB - Institute for Research in Biomedicine [Barcelona, Spain]
8 UMR BGPI - Biologie et Génétique des Interactions Plante-Parasite
9 Color Genomics
10 Pacific Biosciences [Menlo Park]
11 NCI-NIH - National Cancer Institute [Bethesda]
12 CUIMC - Columbia University Irving Medical Center
13 UIUC - University of Illinois at Urbana-Champaign [Urbana]
14 Southwest Research and Outreach Center [Lamberton]
15 UPR - University of Puerto Rico
16 UF - University of Florida [Gainesville]
17 Agricen Sciences
18 USDA-ARS : Agricultural Research Service
19 Penn State - Pennsylvania State University
20 IGEPP - Institut de Génétique, Environnement et Protection des Plantes
21 Unicatt - Università cattolica del Sacro Cuore [Piacenza e Cremona]
22 NDSU - North Dakota State University
23 ISU - Iowa State University
24 Unict - Università degli studi di Catania = University of Catania
25 University of Wisconsin–Milwaukee
26 NSW DPI - New South Wales Department of Primary Industries
27 Michigan State University [East Lansing]
28 UMM - University of Minnesota [Morris]
29 CAS - Chinese Academy of Sciences [Beijing]
30 NTU - National Taiwan University [Taiwan]
31 CEROM - Centre de Recherche sur les Grains [Québec]
32 USDA - United States Department of Agriculture
33 SNU - Seoul National University [Seoul]
34 University of Haifa [Haifa]
35 UNIMORE - Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia
36 Unicatt - Università cattolica del Sacro Cuore [Milano]
37 SDSTATE - South Dakota State University
38 IIT - Illinois Institute of Technology
39 Unhas - Hasanuddin University
40 Cornell AgriTech
41 Department of Entomology [CALS]
42 Texas A&M University [College Station]
43 OSU - The Ohio State University [Columbus]
44 CAAS - Chinese Academy of Agricultural Sciences
2 Know Your Bee Inc
3 JHU - Johns Hopkins University
4 BIST - Barcelona Institute of Science and Technology
5 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
6 CRG-UPF - Center for Genomic Regulation
7 IRB - Institute for Research in Biomedicine [Barcelona, Spain]
8 UMR BGPI - Biologie et Génétique des Interactions Plante-Parasite
9 Color Genomics
10 Pacific Biosciences [Menlo Park]
11 NCI-NIH - National Cancer Institute [Bethesda]
12 CUIMC - Columbia University Irving Medical Center
13 UIUC - University of Illinois at Urbana-Champaign [Urbana]
14 Southwest Research and Outreach Center [Lamberton]
15 UPR - University of Puerto Rico
16 UF - University of Florida [Gainesville]
17 Agricen Sciences
18 USDA-ARS : Agricultural Research Service
19 Penn State - Pennsylvania State University
20 IGEPP - Institut de Génétique, Environnement et Protection des Plantes
21 Unicatt - Università cattolica del Sacro Cuore [Piacenza e Cremona]
22 NDSU - North Dakota State University
23 ISU - Iowa State University
24 Unict - Università degli studi di Catania = University of Catania
25 University of Wisconsin–Milwaukee
26 NSW DPI - New South Wales Department of Primary Industries
27 Michigan State University [East Lansing]
28 UMM - University of Minnesota [Morris]
29 CAS - Chinese Academy of Sciences [Beijing]
30 NTU - National Taiwan University [Taiwan]
31 CEROM - Centre de Recherche sur les Grains [Québec]
32 USDA - United States Department of Agriculture
33 SNU - Seoul National University [Seoul]
34 University of Haifa [Haifa]
35 UNIMORE - Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia
36 Unicatt - Università cattolica del Sacro Cuore [Milano]
37 SDSTATE - South Dakota State University
38 IIT - Illinois Institute of Technology
39 Unhas - Hasanuddin University
40 Cornell AgriTech
41 Department of Entomology [CALS]
42 Texas A&M University [College Station]
43 OSU - The Ohio State University [Columbus]
44 CAAS - Chinese Academy of Agricultural Sciences
Manuella van Munster
- Fonction : Auteur
- PersonId : 744052
- IdHAL : manuellavan-munster
- ORCID : 0000-0002-1635-7915
Anthony Bretaudeau
- Fonction : Auteur
- PersonId : 1688
- IdHAL : anthony-bretaudeau
- ORCID : 0000-0003-0914-2470
- IdRef : 253128358
Fabrice Legeai
- Fonction : Auteur
- PersonId : 1204855
- IdHAL : fabrice-legeai
- ORCID : 0000-0002-6472-4839
- IdRef : 273916432
Résumé
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.