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Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

Alice B. Dennis 1, 2, 3, * Gabriel I. Ballesteros 4, 5 Stéphanie Robin 6, 7 Lukas Schrader 8 Jens Bast 9, 10 Jan Berghöfer 8 Leo Beukeboom 11 Maya Belghazi 12 Anthony Bretaudeau 6, 7 Jan Büllesbach 8 Elizabeth Cash 13 Dominique Colinet 14 Zoé Dumas 9 Patrizia Falabella 15 Jean-Luc Gatti 14 Elzemiek Geuverink 11 Joshua D. Gibson 13, 16 Corinne Hertäg 17, 1 Stefanie Hartmann 3 Emmanuelle Joly 18 Mark Lammers 8 Blas I. Lavandero 5 Ina Lindenbaum 8 Lauriane Galata-Massardier 14 Camille Meslin 18 Nicolas Montagné 18 Nina Pak 13 Marylène Poirie 14 Rosanna Salvia 15 Chris R. Smith 19 Denis Tagu 6 Sophie Tares 14 Heiko Vogel 20 Tanja Schwander 9 Jean-Christophe Simon 6 Christian Figueroa 4, 5 Christoph Vorburger 1, 2 Fabrice Legeai 6, 7 Jürgen Gadau 8
* Corresponding author
1 Department of Aquatic Ecology
2 Institute of Integrative Biology
3 Institute of Biochemistry and Biology
4 Instituto de Ciencias Biológicas
5 Universidad de Talca
6 IGEPP - Institut de Génétique, Environnement et Protection des Plantes
7 UR1 - Université de Rennes 1
8 IEB - Institute for Evolution and Biodiversity
9 Department of Ecology and Evolution
10 University of Cologne
11 University of Groningen
12 AMU - Aix Marseille Université
13 University of California [Berkeley]
14 ISA - Institut Sophia Agrobiotech
15 University of Basilicata
16 University of Georgia [USA]
17 ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich]
18 IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) - Institut d'écologie et des sciences de l'environnement de Paris
19 Earlham College
20 Department of Entomology
Abstract : Background Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biocontrol, and infecting aphids requires overcoming both aphid defenses and their defensive endosymbionts. Results We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp), highly syntenic, and the most AT-rich reported thus far for any arthropod (GC content: 25.8% and 23.8%). This nucleotide bias is accompanied by skewed codon usage, and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and age-specific energy demands. We identify expansions of F-box/Leucine-rich-repeat proteins, suggesting that diversification in this gene family may be associated with their broad host range or with countering defenses from aphids’ endosymbionts. The absence of some immune genes (Toll and Imd pathways) resembles similar losses in their aphid hosts, highlighting the potential impact of symbiosis on both aphids and their parasitoids. Conclusions These findings are of fundamental interest for insect evolution and beyond. This will provide a strong foundation for further functional studies including coevolution with respect to their hosts, the basis of successful infection, and biocontrol. Both genomes are available at https://bipaa.genouest.org.
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Alice B. Dennis, Gabriel I. Ballesteros, Stéphanie Robin, Lukas Schrader, Jens Bast, et al.. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. 2019. ⟨hal-02788571⟩

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