Project description:Nicotiana attenuata and Solanum nigrum were challenged with different insects: Manduca sexta and Tupiocoris notatus in different combinations Goals of the study are first to haracterize the transcriptional response of two native Solanaceous plants (Nicotiana attenuata and Solanum nigrum) to attack from two herbivorous pests common on Solanaceous crops (Manduca sexta and Tupiocoris notatus). And second to identify genes involved in herbivore vaccination phenomenon. After germination, inbred and genetically characterized lines of N. attenuata DI92 and S. nigrum Sn30 originally collected from southwestern Utah in 1988, and Jena Germany in 2000, respectively, were grown in a greenhouse. Eggs of Manduca sexta (abbreviated M. s.) came from the North Carolina State University - Entomology Insectary and were hatched under 37°C. Nymphs and adults of Tupiocoris notatus (abbreviated T. n.) came from laboratory colonies started in 2000 with individuals collected from our Utah field sites. Plant were challenged with these different insect and combinations of them. All plants for a given treatment were enclosed in glass-and-mesh insect cages to avoid cross-infection. After 24 h or 5 days the herbivores and their frass were removed, and the above ground biomass of each plant was flash-frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Three independent replicate cages (biological replicates) were used for each of the 7 treatments resulting in a total of 21 cages per species. RNA extraction was performed according to the protocol using Trizol. The RNA samples represent a pooled sample from 4 plants grown in a cage. Keywords: Direct comparison
Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.