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

Alice Dennis; Gabriel Ballesteros; Stéphanie Robin; Lukas Schrader; Jens Bast; Jan Berghöfer; Leo Beukeboom; Maya Belghazi; Anthony Bretaudeau; Jan Buellesbach; Elizabeth Cash; Dominique Colinet; Zoé Dumas; Mohammed Errbii; Patrizia Falabella; Jean-Luc Gatti; Elzemiek Geuverink; Joshua Gibson; Corinne Hertaeg; Stefanie Hartmann; Emmanuelle Jacquin-Joly; Mark Lammers; Blas Lavandero; Ina Lindenbaum; Lauriane Massardier-Galatà; Camille Meslin; Nicolas Montagné; Nina Pak; Marylène Poirié; Rosanna Salvia; Denis Tagu; Sophie Tares; Heiko Vogel; Tanja Schwander; Jean-Christophe Simon; Christian Figueroa; Christoph Vorburger; Fabrice Legeai; Jürgen Gadau; R.Chris Smith

doi:10.1186/s12864-020-6764-0

Journal articles

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

Alice Dennis ^{1, *} Gabriel Ballesteros ² Stéphanie Robin ^{3, 4} Lukas Schrader ⁵ Jens Bast ⁶ Jan Berghöfer ⁵ Leo Beukeboom ⁷ Maya Belghazi ⁸ Anthony Bretaudeau ³ Jan Buellesbach ⁵ Elizabeth Cash ⁹ Dominique Colinet ¹⁰ Zoé Dumas ⁶ Mohammed Errbii ⁵ Patrizia Falabella ^{11, 4} Jean-Luc Gatti ¹⁰ Elzemiek Geuverink ⁷ Joshua Gibson ^{12, 13} Corinne Hertaeg ¹ Stefanie Hartmann ¹⁴ Emmanuelle Jacquin-Joly ¹⁵ Mark Lammers ¹³ Blas Lavandero ² Ina Lindenbaum ⁵ Lauriane Massardier-Galatà ¹⁰ Camille Meslin ¹⁶ Nicolas Montagné ¹⁵ Nina Pak ⁹ Marylène Poirié ¹⁰ Rosanna Salvia ¹¹ Denis Tagu ⁴ Sophie Tares ¹⁰ Heiko Vogel ¹⁷ Tanja Schwander ⁶ Jean-Christophe Simon ⁴ Christian Figueroa ² Christoph Vorburger ¹¹ Fabrice Legeai ^{4, 18} Jürgen Gadau ^{19, *} R.Chris Smith ²⁰

* Corresponding author

1 Department of Aquatic Ecology - (Dübendorf, Suisse)

2 Universidad de Talca

3 GEF - Plateforme Génomique Environnementale et Fonctionnelle

4 IGEPP - Institut de Génétique, Environnement et Protection des Plantes

5 IEB - Institute for Evolution and Biodiversity

6 DEE - Département d'écologie et évolution [Lausanne]

7 GELIFES - Groningen Institute for Evolutionary Life Sciences [Groningen]

8 INP - Institut de neurophysiopathologie

9 Department of Environmental Sciences [Riverside]

10 ISA - Institut Sophia Agrobiotech

11 UNIBAS - Università degli studi della Basilicata [Potenza]

12 Georgia Southern University

13 University of California [Berkeley]

14 Universität Potsdam

15 PISC - Physiologie de l'Insecte, Signalisation et Communication [Versailles]

16 iEES Paris - Institut d'écologie et des sciences de l'environnement de Paris

17 Max Planck Institute for Chemical Ecology

18 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics

Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE

19 ASU - Arizona State University [Tempe]

20 Department of biology Earlham College, Richmond, IN 47374, USA.

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 biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective 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) 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 energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes.

Conclusions: These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.

Keywords : De novo genome assembly Venom proteins Toll and Imd pathways Parasitoid wasp Lysiphlebus fabarum GC content DNA methylation loss Aphid host Aphidius ervi Chemosensory genes

Document type :

Journal articles

Domain :

Life Sciences [q-bio]

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https://hal.inrae.fr/hal-02649295
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Submitted on : Monday, September 28, 2020 - 4:51:19 PM
Last modification on : Wednesday, May 11, 2022 - 3:20:09 AM

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

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

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