Establishment and analysis of a reference transcriptome for Spodoptera frugiperda

Fabrice Legeai; Sylvie Gimenez; Bernard Duvic; Jean-Michel Escoubas; Anne-Sophie Gosselin Grenet; Florence Blanc; François Cousserans; Imène Séninet; Anthony Bretaudeau; Doriane Mutuel; Pierre-Alain Girard; Christelle Monsempes; Ghislaine Magdelenat; Frédérique Hilliou; René Feyereisen; Mylène Ogliastro; Anne-Nathalie Volkoff; Emmanuelle Jacquin-Joly; Emmanuelle d'Alençon; Nicolas Nègre; Philippe Fournier

doi:10.1186/1471-2164-15-704

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda

Fabrice Legeai ^{1, 2} Sylvie Gimenez ³ Bernard Duvic ³ Jean-Michel Escoubas ³ Anne-Sophie Gosselin Grenet ³ Florence Blanc ³ François Cousserans ³ Imène Séninet ³ Anthony Bretaudeau ^{1, 4} Doriane Mutuel ³ Pierre-Alain Girard ³ Christelle Monsempes ⁵ Ghislaine Magdelenat ⁶ Frédérique Hilliou ⁷ René Feyereisen ³ Mylène Ogliastro ³ Anne-Nathalie Volkoff ³ Emmanuelle Jacquin-Joly ⁵ Emmanuelle d'Alençon ³ Nicolas Nègre ^{3, 8, *} Philippe Fournier ³

* Corresponding author

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

2 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics

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

3 DGIMI - Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier]

4 Plateforme bioinformatique GenOuest [Rennes]

Inria Rennes – Bretagne Atlantique , Plateforme Génomique Santé Biogenouest®, UR1 - Université de Rennes 1, IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires

5 IEES - Institut d'écologie et des sciences de l'environnement de Paris

6 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]

7 ISA - Institut Sophia Agrobiotech [Sophia Antipolis]

8 IUF - Institut Universitaire de France

Abstract : Background
Spodoptera frugiperda (Noctuidae) is a major agricultural pest throughout the American continent. The highly polyphagous larvae are frequently devastating crops of importance such as corn, sorghum, cotton and grass. In addition, the Sf9 cell line, widely used in biochemistry for in vitro protein production, is derived from S. frugiperda tissues. Many research groups are using S. frugiperda as a model organism to investigate questions such as plant adaptation, pest behavior or resistance to pesticides.
Results
In this study, we constructed a reference transcriptome assembly (Sf_TR2012b) of RNA sequences obtained from more than 35 S. frugiperda developmental time-points and tissue samples. We assessed the quality of this reference transcriptome by annotating a ubiquitous gene family - ribosomal proteins - as well as gene families that have a more constrained spatio-temporal expression and are involved in development, immunity and olfaction. We also provide a time-course of expression that we used to characterize the transcriptional regulation of the gene families studied.
Conclusion
We conclude that the Sf_TR2012b transcriptome is a valid reference transcriptome. While its reliability decreases for the detection and annotation of genes under strong transcriptional constraint we still recover a fair percentage of tissue-specific transcripts. That allowed us to explore the spatial and temporal expression of genes and to observe that some olfactory receptors are expressed in antennae and palps but also in other non related tissues such as fat bodies. Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

Document type :

Journal articles

Domain :

Life Sciences [q-bio] / Biochemistry, Molecular Biology / Genomics [q-bio.GN]

Complete list of metadatas

https://hal.inria.fr/hal-01058982
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Submitted on : Friday, August 29, 2014 - 1:05:08 AM
Last modification on : Thursday, October 10, 2019 - 11:36:02 AM
Long-term archiving on: Sunday, November 30, 2014 - 10:10:30 AM

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda

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Establishment and analysis of a reference transcriptome for Spodoptera frugiperda

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