De novo characterization of western flower thrips (Frankliniella occidentalis) transcriptome and comparasive analysis of the gene expression profile between tomato spotted wilt virus(TSWV) infected and non-infected population.

The western flower thrips (WFT), Frankliniella occidentalis (Pergande) (Thysan., Thripae), an invasive insect around world, causes plant damage not only by directly feeding, but also by indirectly vectoring Tospoviruses, such as tomato spotted wilt virus (TSWV). High level of resistance to insecticides is a main factor that contributes to WFT as an invasive species worldwide. Despite being an important pest in agricultural ecosystem, gene information for F. occidentalis, and for thrips in general, has been scant. Herein, we used RNA-Seq on Illumina sequencing platform to characterize the transcriptome WFT and identify its gene expression associated with insecticide resistance and virus transmission. In total, we compiled 59,932unigenes with an average length of 565 bp for WFT. Sequence similarity analysis against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found that 36,339unigenes could be annotated with gene descriptions and conserved protein domains. Among the known proteins, 7,432 were assigned to gene ontology; 17,620 had significant matches in the KEGG database and were assigned to 220 KEGG pathways, and among them, 2,521unigenes were assigned to the metabolic pathways,which was the largest group,followed by amoebiasis, spliceosome, and vibrio cholerae infection pathway, having 894unigenes, 803unigenes, and 781unigenes respectively. Within these transcripts, we identified 1,246 potential microsatellite loci and 18,825 single nucleotide polymorphisms, which are useful for studying the adaptation and ecology of WFT. Moreover, we did comparative analysis of gene expression profile between TSWV infected and non-infected WFT population. And the result demonstrated that some immune regulatory systems, such as RNA interference, JAK/STAT, Toll pathway, and some disease infection pathway, such as amoebiasis, vibrio cholerae infection pathway, were up-regulated in TSWV infected WFT.This data represents the most comprehensive genomic resource for F. occidentalis to date, which provides an invaluable resource for WFT molecular mechanisms of insecticide resistant and population genetic analysis, as well as for future F. occidentalis and other thrips genome annotation. Pathway mapping and gene expression profile analysis of TSWV infected and non-infected F. occidentalis shed light on the molecular bases of TSWV-WFT interaction.