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Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

Legeai F, Gimenez S, Duvic B, Escoubas JM, Gosselin Grenet AS, Blanc F, Cousserans F, Séninet I, Bretaudeau A, Mutuel D, Girard PA, Monsempes C, Magdelenat G, Hilliou F, Feyereisen R, Ogliastro M, Volkoff AN, Jacquin-Joly E, d'Alençon E, Nègre N, Fournier P - BMC Genomics (2014)

Bottom Line: 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.Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR1333, DGIMI, Montpellier, France. nicolas.negre@univ-montp2.fr.

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.

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Related in: MedlinePlus

Schematic representation ofS. frugiperdaimmune components found in Sf_TR2012b. The four main signaling pathways involved in insect immune response are detailed as well as the pro-PO cascade. The negative regulators are red circled and the components that were not found in Sf_TR2012b are indicated by red arrows.
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Fig2: Schematic representation ofS. frugiperdaimmune components found in Sf_TR2012b. The four main signaling pathways involved in insect immune response are detailed as well as the pro-PO cascade. The negative regulators are red circled and the components that were not found in Sf_TR2012b are indicated by red arrows.

Mentions: Finally, we tried to annotate most of the immune-related genes of FAW using Sf_TR2012b. The invertebrate immune response has been extensively studied in insects and today it is in the insect model, D. melanogaster, that we have the most integrated understanding of this physiological function. Indeed, biochemical, genetic and molecular biology approaches have led to the characterization of the molecular mechanisms involved in (i) pathogen recognition and extra-cellular signaling, (ii) signal transduction through intra-cellular signaling pathways, and (iii) pathogen elimination through the production of effectors molecules and cell activation (for review see [24, 25]). We inventoried the components of S. frugiperda immune repertoire by comparing Sf_TR2012b with the immune repertoire described for D. melanogaster and other insects [26–30] and classified them in three groups (Additional file 6: Table S5). The first one contains transcripts encoding proteins involved in pathogen recognition as well as extracellular molecules associated to signal transduction. The second group contains proteins belonging to intra cellular signaling pathways which control among others the antifungal, antibacterial and antiviral responses and that also play a key role in developmental processes (Toll, Imd, JAK/STAT and JNK). The third group contains an inventory of effectors of the immune response (mainly anti-microbial peptides, AMPs). As summarized in Figure 2, we were able to identify in S. frugiperda transcriptome most of the components involved in the Drosophila immune response (73 out of 79). Two of the missing components were located on the Toll pathway. The first one, Grass is a serine protease involved in the activation of spätzle processing enzyme. Grass belongs to a large family of CLIP domain containing proteases. In Sf_TR2012b, we identified 16 such proteases while 15 and 37 were found in the genomes of B. mori and D. melanogaster, respectively. Therefore, even though Grass might be one of them, we were not able to identify it with certainty. The second one is the Dorsal-related immunity factor, Dif, which, to our knowledge, was characterized only in Diptera. Three components of the Imd pathway, the inhibitor of kinase kinase gamma also known as Kenny in Drosophila, the caspase Dredd and the negative regulatory factor PIRK were not found. The last missing component is the cytokine Upd3, an activator of the JAK/STAT pathway which was also characterized only in Diptera.Figure 2


Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

Legeai F, Gimenez S, Duvic B, Escoubas JM, Gosselin Grenet AS, Blanc F, Cousserans F, Séninet I, Bretaudeau A, Mutuel D, Girard PA, Monsempes C, Magdelenat G, Hilliou F, Feyereisen R, Ogliastro M, Volkoff AN, Jacquin-Joly E, d'Alençon E, Nègre N, Fournier P - BMC Genomics (2014)

Schematic representation ofS. frugiperdaimmune components found in Sf_TR2012b. The four main signaling pathways involved in insect immune response are detailed as well as the pro-PO cascade. The negative regulators are red circled and the components that were not found in Sf_TR2012b are indicated by red arrows.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4150953&req=5

Fig2: Schematic representation ofS. frugiperdaimmune components found in Sf_TR2012b. The four main signaling pathways involved in insect immune response are detailed as well as the pro-PO cascade. The negative regulators are red circled and the components that were not found in Sf_TR2012b are indicated by red arrows.
Mentions: Finally, we tried to annotate most of the immune-related genes of FAW using Sf_TR2012b. The invertebrate immune response has been extensively studied in insects and today it is in the insect model, D. melanogaster, that we have the most integrated understanding of this physiological function. Indeed, biochemical, genetic and molecular biology approaches have led to the characterization of the molecular mechanisms involved in (i) pathogen recognition and extra-cellular signaling, (ii) signal transduction through intra-cellular signaling pathways, and (iii) pathogen elimination through the production of effectors molecules and cell activation (for review see [24, 25]). We inventoried the components of S. frugiperda immune repertoire by comparing Sf_TR2012b with the immune repertoire described for D. melanogaster and other insects [26–30] and classified them in three groups (Additional file 6: Table S5). The first one contains transcripts encoding proteins involved in pathogen recognition as well as extracellular molecules associated to signal transduction. The second group contains proteins belonging to intra cellular signaling pathways which control among others the antifungal, antibacterial and antiviral responses and that also play a key role in developmental processes (Toll, Imd, JAK/STAT and JNK). The third group contains an inventory of effectors of the immune response (mainly anti-microbial peptides, AMPs). As summarized in Figure 2, we were able to identify in S. frugiperda transcriptome most of the components involved in the Drosophila immune response (73 out of 79). Two of the missing components were located on the Toll pathway. The first one, Grass is a serine protease involved in the activation of spätzle processing enzyme. Grass belongs to a large family of CLIP domain containing proteases. In Sf_TR2012b, we identified 16 such proteases while 15 and 37 were found in the genomes of B. mori and D. melanogaster, respectively. Therefore, even though Grass might be one of them, we were not able to identify it with certainty. The second one is the Dorsal-related immunity factor, Dif, which, to our knowledge, was characterized only in Diptera. Three components of the Imd pathway, the inhibitor of kinase kinase gamma also known as Kenny in Drosophila, the caspase Dredd and the negative regulatory factor PIRK were not found. The last missing component is the cytokine Upd3, an activator of the JAK/STAT pathway which was also characterized only in Diptera.Figure 2

Bottom Line: 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.Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR1333, DGIMI, Montpellier, France. nicolas.negre@univ-montp2.fr.

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.

Show MeSH
Related in: MedlinePlus