Project description:Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were fed six different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness. Science for Life Laboratory (SciLifeLab, Sweden) conducted the sequencing of RNA samples. The cDNA libraries (Illumina TruSeq RNA) were sequenced using the Illumina HiSeq 2000 platform using 100-bp paired-end sequencing. We obtained more than 9 million read-pairs from seventy one cDNA libraries sequenced and the transcriptome assembly (TA) of these sequences resulted in 213, 237 transcripts (162,189 components) with a contig N50 of 2,193 bp. Thus, we covered approximately 300x the transcriptome of caterpillars of the species V. cardui.
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.
Project description:Butterfly wing patterns are an important model for studying the genetic basis of morphological evolution. Here we used RNA-seq expression profiling in the butterfly Vanessa cardui to characterize the transcriptional basis of wing pigmentation. This approach identified numerous candidate genes including known and suspected components of the insect melanin and ommochrome biosynthetic pathways.
