Project description:Cymbopogon spp. are grass species widely used around the world as medicinal plants and in various industries for the production of perfumes and pharmaceuticals. Despite their extensive use, there are relatively few studies at the genomic and transcriptomic levels. In this study, transcriptomic data were generated for two species—Cymbopogon flexuosus and Cymbopogon winterianus—to investigate evolutionary aspects and the expression of genes associated with secondary metabolite biosynthesis. The transcriptome assembly revealed a total of 18,286 and 22,458 transcripts for C. flexuosus and C. winterianus, respectively. Furthermore, the reads were mapped against the genomes of related species, including Andropogon gerardii, Sorghum bicolor, Saccharum officinarum, Miscanthus sinensis, Miscanthus lutarioriparius, and Zea mays, to assess their conservation across these genomes. The results indicated which species are more closely related to the Cymbopogon genus and highlighted key differences in metabolic pathways.
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.
