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Journal articles
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
2
GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
4
Plateforme bioinformatique GenOuest [Rennes]
UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Fabrice Legeai 1, 2
Author
Sylvie Gimenez 3
Author
Bernard Duvic 3
Author IdHAL : bernard-duvic ORCID : https://orcid.org/0000-0002-7618-7719
Jean-Michel Escoubas 3
Author
Anne-Sophie Gosselin Grenet 3
Author
Florence Blanc 3
Author
François Cousserans 3
Author
Imène Séninet 3
Author
Anthony Bretaudeau 1, 4
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : anthony-bretaudeau
Doriane Mutuel 3
Author
Pierre-Alain Girard 3
Author
Christelle Monsempes 5
Author
Ghislaine Magdelenat 6
Author
Frédérique Hilliou 7
Author
René Feyereisen 3
Author
Mylène Ogliastro 3
Author IdHAL : mylene-ogliastro IdRef : https://www.idref.fr/167635050 ORCID : https://orcid.org/0000-0003-4841-7043
Anne-Nathalie Volkoff 3
Author IdHAL : anne-nathalie-volkoff ORCID : https://orcid.org/0000-0002-7211-1370
Emmanuelle Jacquin-Joly 5
Author IdHAL : emmanuelle-joly ORCID : https://orcid.org/0000-0002-6904-2036
Emmanuelle d'Alençon 3
Author
Nicolas Nègre 3, 8
Correspondent author IdHAL : nicolas-negre ORCID : https://orcid.org/0000-0001-9727-3416
Philippe Fournier 3
Author
1
IGEPP - Institut de Génétique, Environnement et Protection des Plantes (Domaine de la Motte au Vicomte BP 35327
35653 Le Rheu - France)
- INRA - Institut National de la Recherche Agronomique : UMR1349 (France)
- UR1 - Université de Rennes 1 : UMR1349 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- AGROCAMPUS OUEST : UMR1349 (Institut Supérieur des Sciences Agronomiques, Agroalimentaires, Horticoles et du Paysage - 65, rue de St Brieuc - CS 84215 - 35042 Rennes cedex - France)
2
GenScale - Scalable, Optimized and Parallel Algorithms for Genomics (Campus de Beaulieu 35042 Rennes cedex - France)
- Inria Rennes – Bretagne Atlantique (Campus de beaulieu
35042 Rennes cedex - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE (France)
- IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
- CentraleSupélec (3, rue Joliot Curie, Plateau de Moulon, 91192 GIF-SUR-YVETTE Cedex - France)
- Télécom Bretagne (Technopôle Brest-Iroise CS 83818 29238 BREST Cedex 3 - France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- ENS Rennes - École normale supérieure - Rennes (Campus de Ker Lann - avenue Robert Schuman - 35170 Bruz - France)
- UBS - Université de Bretagne Sud (BP 92116 - 56321 Lorient cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR6074 (France)
- INSA Rennes - Institut National des Sciences Appliquées - Rennes (20, avenue des Buttes de Coësmes - CS 70839 - 35708 Rennes cedex 7 - France)
- IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
3
DGIMI - Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (Place Eugène Bataillon 34095 Montpellier cedex 5 - France)
- INRA - Institut National de la Recherche Agronomique : UMR1333 (France)
- UM2 - Université Montpellier 2 - Sciences et Techniques (Place Eugène Bataillon - 34095 Montpellier cedex 5 - France)
- UM - Université de Montpellier (163 rue Auguste Broussonnet - 34090 Montpellier - France)
4
Plateforme bioinformatique GenOuest [Rennes] (France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- Plateforme Génomique Santé Biogenouest® (France)
- Inria Rennes – Bretagne Atlantique (Campus de beaulieu
35042 Rennes cedex - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE (France)
- IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
- CentraleSupélec (3, rue Joliot Curie, Plateau de Moulon, 91192 GIF-SUR-YVETTE Cedex - France)
- Télécom Bretagne (Technopôle Brest-Iroise CS 83818 29238 BREST Cedex 3 - France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- ENS Rennes - École normale supérieure - Rennes (Campus de Ker Lann - avenue Robert Schuman - 35170 Bruz - France)
- UBS - Université de Bretagne Sud (BP 92116 - 56321 Lorient cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR6074 (France)
- INSA Rennes - Institut National des Sciences Appliquées - Rennes (20, avenue des Buttes de Coësmes - CS 70839 - 35708 Rennes cedex 7 - France)
- IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
5
iEES - Institut d'écologie et des sciences de l'environnement de Paris (UPMC, campus de Jussieu - Paris (75005) - AgroParisTech-INRA - Grignon (78) - INRA - Versailles (78) - IRD - Bondy (93) - U-PEC - Créteil (94)
- France)
- INRA - Institut National de la Recherche Agronomique : UMR1392 (France)
- UPMC - Université Pierre et Marie Curie - Paris 6 : UMR113 (4 place Jussieu - 75005 Paris - France)
- UPEC UP12 - Université Paris-Est Créteil Val-de-Marne - Paris 12 : UMR7618 (61 avenue du Général de Gaulle - 94010 Créteil cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR7618 (France)
6
GENOSCOPE - Genoscope - Centre national de séquençage [Evry] (2, rue Gaston Crémieux CP5706 91057 EVRY Cedex - France)
- Université Paris-Saclay (Bâtiment Bréguet, 3 Rue Joliot Curie 2e ét, 91190 Gif-sur-Yvette - France)
- DRF (CEA) - Direction de Recherche Fondamentale (CEA) : DRF/JACOB (Direction de Recherche Fondamentale
Fundamental Research Division
CEA Saclay
91191 Gif-sur-Yvette
- France)
- CEA - Commissariat à l'énergie atomique et aux énergies alternatives (Centre de Saclay Centre de Grenoble Centre de Cadarache etc - France)
7
ISA - Institut Sophia Agrobiotech (INRA Centre de recherche Provence-Alpes-Côte d'Azur 400, route des Chappes BP 167 06903 Sophia Antipolis Cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR7254 (France)
- UNS - Université Nice Sophia Antipolis (... - 2019) (Parc Valrose - BP 2135 - 06103 Nice cedex 2 - France)
- COMUE UCA - COMUE Université Côte d'Azur (2015-2019) (Parc Valrose, 28, avenue Valrose 06108 Nice Cedex 2 - France)
- INRA - Institut National de la Recherche Agronomique : UMR1355 (France)
8
IUF - Institut Universitaire de France (Maison des Universités 103 Boulevard Saint-Michel 75005 Paris - France)
- M.E.N.E.S.R. - Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (1 rue Descartes - 75231 Paris cedex 05 - 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.
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.
Mots-clés :
Spodoptera frugiperda
transcriptomics
Document type :
Journal articles
Complete list of metadata
https://hal.inria.fr/hal-01058982
Contributor : Ed. Bmc Connect in order to contact the contributor
Submitted on : Friday, August 29, 2014 - 1:05:08 AM
Last modification on : Thursday, January 27, 2022 - 3:28:02 AM
Long-term archiving on: : Sunday, November 30, 2014 - 10:10:30 AM
Contributor : Ed. Bmc Connect in order to contact the contributor
Submitted on : Friday, August 29, 2014 - 1:05:08 AM
Last modification on : Thursday, January 27, 2022 - 3:28:02 AM
Long-term archiving on: : Sunday, November 30, 2014 - 10:10:30 AM
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Identifiers
- HAL Id : hal-01058982, version 1
- DOI : 10.1186/1471-2164-15-704
- PRODINRA : 269917
- PUBMED : 25149648
- WOS : 000341039500001
Collections
IRISA | INRIA | CNRS | UNIV-RENNES1 | CEA | UNAM | INRA | IRISA-D7 | INSTITUT-TELECOM | UPMC | IEES | AGROPOLIS | UPEC-UPEM | BIOSIT | UR1-UFR-SVE | UR1-MATH-STIC | UR1-UFR-ISTIC | BA | UNIV-MONTPELLIER | UNIV-COTEDAZUR | JACOB | CEA-DRF | UNIV-RENNES | DGIMI | SORBONNE-UNIVERSITE | SU-SCIENCES | UPEC | GENOSCOPE | INRAE | UP-SCIENCES | INRAEOCCITANIEMONTPELLIER | INSA-RENNES | SU-TI | UR1-ENV | UR1-MATH-NUM | UNIV-PARIS | EC-PARIS
Citation
Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin Grenet, et al.. Establishment and analysis of a reference transcriptome for Spodoptera frugiperda. BMC Genomics, BioMed Central, 2014, 15 (1), pp.704. ⟨10.1186/1471-2164-15-704⟩. ⟨hal-01058982⟩
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