Establishment and analysis of a reference transcriptome for Spodoptera frugiperda
1 INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, France
2 INRIA, IRISA, Genscale, Campus Beaulieu, Rennes, France
3 INRA, UMR1333, DGIMI, Montpellier, France
4 Université Montpellier 2, UMR1333, DGIMI, Montpellier, France
5 INRIA, IRISA, Genouest, Campus Beaulieu, Rennes, France
6 INRA, UMR 1392, Institut d’Ecologie et des Sciences de l’Environnement de Paris (iEES-Paris), Versailles, France
7 Genoscope, Evry, France
8 INRA - CNRS - Univ.Nice Sophia Antipolis, UMR Institut Sophia Agrobiotech (ISA), Sophia Antipolis, France
9 Institut Universitaire de France (IUF), Paris, France
BMC Genomics 2014, 15:704 doi:10.1186/1471-2164-15-704Published: 23 August 2014
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.
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.
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.