Project description:Corals in nearshore marine environments are increasingly exposed to reduced water quality, which is the major local threat to coral reefs in Hawaii. Corals surviving in such conditions may have adapted to withstand sedimentation, pollutants, and other environmental stressors. Lobe coral (Porites lobata) populations from Maunalua Bay, Hawaii showed clear genetic differentiation along with distinct cellular protein expressions between the 'polluted, high-stress' nearshore site and the 'low-stress' offshore site. To understand the driving force of the observed genetic partitioning, reciprocal transplant and common-garden experiments were conducted using the nearshore and offshore colonies of P. lobata from Maunalua Bay to assess phenotypic differences between the two coral populations. Stress-related physiological and molecular responses were compared between the two populations. Proteomic responses highlighted the inherent differences in the cellular metabolic state and activities between the two populations under the same environmental conditions; nearshore corals did not significantly alter their proteome between the sites, while offshore corals responded to the nearshore transplantation with increased abundances of proteins associated with detoxification, antioxidant, and various metabolic processes. The response differences across multiple phenotypes suggest that the observed genetic partitioning was likely due to local adaptation.
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.