Project description:The analysis of the mapped QTLs and their genetic dissection in the US grown japonica rice genotypes, Cypress and Lagrue at genomic and transcriptomic levels The gene expression profiling using Deseq was performed using data collected under control and heat stress For heat stress:a day/night temperature of 30°C (86°F)/28°C (82.4°F) for 10 h (20:00–6:00) was maintained while the control treatment was set at a day/night temperature of 30°C (86°F)/22.2°C (72°F) until harvest maturity (approximately 18–20% grain moisture content)
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:Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post inoculation with Azoarcus olearius BH72, the goal is to understand the transcriptomic response of rice roots to colonization by bacterial endophyte
