Limits...
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.

Show MeSH

Related in: MedlinePlus

Tissue specific expression of chemosensory genes and anti-microbial peptides. A. Heatmap showing the expression as row scaled z-scores of S. frugiperda odorant-binding proteins, chemosensory proteins, olfactory receptors and ionotropic receptors in the 10 Illumina RNAseq experiments. A higher expression of odorant-binding proteins in the antennae and palps can be observed. B. Same as in A. for the anti-microbial peptides identified in S. frugiperda transcriptome. A higher expression of AMP in induced fat bodies is observed as well as an overexpression in antennae and palps as well as in tracheae, two tissues in contact with the external environment.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Tissue specific expression of chemosensory genes and anti-microbial peptides. A. Heatmap showing the expression as row scaled z-scores of S. frugiperda odorant-binding proteins, chemosensory proteins, olfactory receptors and ionotropic receptors in the 10 Illumina RNAseq experiments. A higher expression of odorant-binding proteins in the antennae and palps can be observed. B. Same as in A. for the anti-microbial peptides identified in S. frugiperda transcriptome. A higher expression of AMP in induced fat bodies is observed as well as an overexpression in antennae and palps as well as in tracheae, two tissues in contact with the external environment.

Mentions: Both antennae and maxillary palps house olfactory neurons that detect odorant volatile molecules via different steps, each involving a specific family of proteins. As expected for proteins involved in olfaction, most of the OBPs and CSPs are highly expressed in antennae and palps (Figure 6A). Interestingly, while most of the OBPs expression was not visible when entire animals were used for RNA extraction (transcript “dilution”), many CSP transcripts could still be highly visible in different samples, suggesting that their expression is not restricted to the olfactory organs. This correlates well with some evidences that CSP function would not be restricted to olfaction [38, 39] and that these proteins would act in fact as general carriers of hydrophobic molecules throughout the insect body. Interestingly, the expression of some ORs was not restricted to the olfactory organs and several could be observed as expressed in the fat body or the midgut (Figure 6A). Such ectopic expression has been already described for some ORs in insects, for instance in B. mori abdmonen [40] and gut [22] and in S. littoralis abdomen and brain [10, 11], although the function of ORs in such organs is still unknown. IR25a showed a broad expression, as already observed in S. littoralis[41].Figure 6


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)

Tissue specific expression of chemosensory genes and anti-microbial peptides. A. Heatmap showing the expression as row scaled z-scores of S. frugiperda odorant-binding proteins, chemosensory proteins, olfactory receptors and ionotropic receptors in the 10 Illumina RNAseq experiments. A higher expression of odorant-binding proteins in the antennae and palps can be observed. B. Same as in A. for the anti-microbial peptides identified in S. frugiperda transcriptome. A higher expression of AMP in induced fat bodies is observed as well as an overexpression in antennae and palps as well as in tracheae, two tissues in contact with the external environment.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Tissue specific expression of chemosensory genes and anti-microbial peptides. A. Heatmap showing the expression as row scaled z-scores of S. frugiperda odorant-binding proteins, chemosensory proteins, olfactory receptors and ionotropic receptors in the 10 Illumina RNAseq experiments. A higher expression of odorant-binding proteins in the antennae and palps can be observed. B. Same as in A. for the anti-microbial peptides identified in S. frugiperda transcriptome. A higher expression of AMP in induced fat bodies is observed as well as an overexpression in antennae and palps as well as in tracheae, two tissues in contact with the external environment.
Mentions: Both antennae and maxillary palps house olfactory neurons that detect odorant volatile molecules via different steps, each involving a specific family of proteins. As expected for proteins involved in olfaction, most of the OBPs and CSPs are highly expressed in antennae and palps (Figure 6A). Interestingly, while most of the OBPs expression was not visible when entire animals were used for RNA extraction (transcript “dilution”), many CSP transcripts could still be highly visible in different samples, suggesting that their expression is not restricted to the olfactory organs. This correlates well with some evidences that CSP function would not be restricted to olfaction [38, 39] and that these proteins would act in fact as general carriers of hydrophobic molecules throughout the insect body. Interestingly, the expression of some ORs was not restricted to the olfactory organs and several could be observed as expressed in the fat body or the midgut (Figure 6A). Such ectopic expression has been already described for some ORs in insects, for instance in B. mori abdmonen [40] and gut [22] and in S. littoralis abdomen and brain [10, 11], although the function of ORs in such organs is still unknown. IR25a showed a broad expression, as already observed in S. littoralis[41].Figure 6

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