Within consortium 4 of BIOACID II, we examine effects of ocean warming and acidification (OWA) on different cod species: Polar cod, Boreogadus saida, and Atlantic cod, Gadus morhua. Species distribution as well as population structure of both are reported to be already changing, mainly driven by warming of water masses in their natural habitats. Shifts of G. morhua into higher latitudes will increasingly interact/interfere with populations of B. saida in Arctic waters. However, it is unclear, by which dynamics and how fast the intersecting area of both species will alter during the next decades, which could even lead to extinction of the cold-adapted native species. Within this work package stock distribution patterns are monitored by means of population genetic analyses of hundreds of samples collected from the beginning in the early nineties of the last century until today to assess the current situation and to project future species occurrences. Complementary to these studies is the physiological characterization of each species by means of incubation experiments. These are used to qualify their robustness/vulnerability to future conditions in the northern oceans on multiple levels of organization, i.e. at whole animal down to the molecular level, studying energy budgets and metabolic regulation as well as effects of OWA on different life stages (work packages 4.1 – 4.7). At first, specimens of B. saida have been under study to evaluate critical levels of OWA. Animals caught this January in the Barents Sea north of Norway were brought to Bremerhaven and incubated for 3 months under different CO2 and temperature combinations. During the incubation period, growth data (WP 4.1) and behavioural patterns (WP 4.6) were collected. Furthermore, samples were taken to monitor the total energy budget (EB) (WP 4.1), cellular and mitochondrial energy budget (WP 4.2) as well as for molecular studies of marker metabolites (WP 4.6) and transcriptomic analyses (this work package, 4.3). In parallel, we set up the basis for comparative protein and DNA sequence analyses for both species by constructing normalized cDNA libraries, which were sequenced with Illumina MiSeq (paired end). In total, sequencing output consists of 3.8 and 2.5 Gbp for B. saida and G. morhua, respectively. Transcripts were assembled using Trinity providing approx. 16k protein sequences for each species with an intersecting sequence amount of 14,843 orthologs. The latter will be analyzed for differences in amino acid usage and codon usage by large-scale comparison. Our working hypothesis is that the different habitat conditions have left adaptational signatures in codon and amino acid usage, which reflect different plasticities for acclimation in both species at the molecular level. Moreover, we would expect the regulation of functional genes in the transcriptomes to be differing, due to different critical thresholds of environmental factors and due to the different evolutionary pressures on metabolic genes. Consensus sequences of both library assemblies are used to build a compact Gadus spec. microarray matching sequence identities of both species to equal amounts. This array will be used to monitor long-term effects of different treatments on the transcriptome of B. saida and will provide an application that will also be used for samples of the planned incubation of specimens of G. morhua in 2014. Together with the collected physiological parameters, population genetics and transcriptomic data will provide an integrated picture of species fitness, critical thresholds of environmental conditions as well as consequences of synergistic effects caused by elevated temperature and high CO2 concentrations.