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The Tara Pacifc expedition (2016–2018) provided an opportunity to investigate calcifcation patterns in extant corals throughout thePacifc Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected fromdiferent environments to assess calcifcation parameters of long-lived reef-building corals. In this study, we compared the calcifcation and carbonate chemistryup-regulation of Diploastrea heliopora and Porites corals from across a range of environments. To this, we analyzed the skeletal geochemistry and growth parameters of 39 colonies of Porites (n=33) and Diploastrea (n=6) collected across the tropical Pacifc Ocean during the Tara Pacifc expedition (2016–2018). Te collected corals represent a suite of cores exposed to various hydrological conditions of seawater temperature (SST: 22.4–29.8 °C), salinity (SSS: 31.5–36.1), and carbonate chemistry (total scale pHsw: 8.01–8.09). Te average chemical composition of the calcifying fuid (pHcf, [CO32−]cf, DICcf, Ωcf) was derived from paired boron isotope (δ11B) and B/Ca analyses of core-top samples corresponding to the last 6 years of growth (2010–2016). Based on these data, we assessed the impact of the ambient seawater properties (SST, salinity, carbonate chemistry) on the cf composition of these slow-growing reef-building genera at the Pacifc basin scale. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2024-04-08.

Current velocities of the upper water column along the cruise track of R/V Meteor cruise M197 were collected by a vessel-mounted 75 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 5.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 8.00 m, a blanking distance of 4.00 m, and a total of 100 bins, covering the depth range between 17.0 m and 809.0 m. Heading, pitch and roll data from the ship's motion reference unit and the navigation data from the Global Positioning systems were used by the data acquisition software VmDAS internally to convert ADCP velocities into earth coordinates. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (-0.1521° +/- 0.5577°) and scale factor (1.0055 +/- 0.0082) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 120 s. Velocity quality flagging is based on different threshold criteria: Depth cells with ensemble-averaged percent-good values below 25% are marked as 'bad data'. Depth cells with velocities above 0.8 m/s are flagged as 'bad data'. Depth cells with a root-mean-square deviation between the measured ensemble-average velocity and a cell-wise running-mean velocity above 0.2 m/s are flagged as 'probably bad data'.

Current velocities of the upper water column along the cruise track of R/V Meteor cruise M197 were collected by a vessel-mounted 38 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 5.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 16.00 m, a blanking distance of 8.00 m, and a total of 80 bins, covering the depth range between 29.0 m and 1293.0 m. Heading, pitch and roll data from the ship's motion reference unit and the navigation data from the Global Positioning systems were used by the data acquisition software VmDAS internally to convert ADCP velocities into earth coordinates. Single-ping data were screened for bottom signals and, where appropriate, a bottom mask was manually processed. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (-44.8506° +/- 0.5350°) and scale factor (1.0005 +/- 0.0083) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 120 s. Velocity quality flagging is based on different threshold criteria: Depth cells with ensemble-averaged percent-good values below 25% are marked as 'bad data'. Depth cells with velocities above 0.8 m/s are flagged as 'bad data'. Depth cells with a root-mean-square deviation between the measured ensemble-average velocity and a cell-wise running-mean velocity above 0.2 m/s are flagged as 'probably bad data'.

Raw water column data were collected aboard RV METEOR during cruise M197 using a Kongsberg EM 122 multibeam echosounder. The expedition took place during 30.12.2023 - 06.02.2024 from Limassol (Republic of Cyprus) to Catania (Italy) in the Mediterranean. The overarching aim was to use the rapidly changing Eastern Mediterranean Sea (EMS) as a natural laboratory to gain mechanistic understanding of biogeochemical and ecosystem transitions of a future (sub-)tropical ocean affected by global warming and other anthropogenic pressures. The M197 cruise on RV Meteor has the following objectives: (i) characterising nutrient biogeochemistry and phytoplankton nutrient limitation of seawaters in the Eastern Mediterranean Sea, (ii) documenting in detail the microbial communities that inhabit these waters from the surface ocean to sediments, (iii) assessing mechanistic connections between nutrient biogeochemistry, surface ocean productivity, deeper water metabolism, and shelf sediments in the cycling of carbon and major nutrients, (iv) using the sedimentary record to assess past environmental change in the EMS. Data were recorded within the EEZs of Greece and Cyprus. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project and published according to the FAIR principles. These data should not be used for navigational purposes.

Raw multibeam bathymetry data were collected aboard RV METEOR during cruise M197 using a Kongsberg EM 710 multibeam echosounder. The expedition took place during 30.12.2023 - 06.02.2024 from Limassol (Republic of Cyprus) to Catania (Italy) in the Mediterranean. The overarching aim was to use the rapidly changing Eastern Mediterranean Sea (EMS) as a natural laboratory to gain mechanistic understanding of biogeochemical and ecosystem transitions of a future (sub-)tropical ocean affected by global warming and other anthropogenic pressures. The M197 cruise on RV Meteor has the following objectives: characterising nutrient biogeochemistry and phytoplankton nutrient limitation of seawaters in the Eastern Mediterranean Sea, (ii) documenting in detail the microbial communities that inhabit these waters from the surface ocean to sediments, (iii) assessing mechanistic connections between nutrient biogeochemistry, surface ocean productivity, deeper water metabolism, and shelf sediments in the cycling of carbon and major nutrients, (iv) using the sedimentary record to assess past environmental change in the EMS. Data were recorded within the EEZs of Greece and Cyprus. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project and published according to the FAIR principles. These data should not be used for navigational purposes.

Raw multibeam bathymetry data were collected aboard RV METEOR during cruise M197 using a Kongsberg EM 122 multibeam echosounder. The expedition took place during 30.12.2023 - 06.02.2024 from Limassol (Republic of Cyprus) to Catania (Italy) in the Mediterranean. The overarching aim was to use the rapidly changing Eastern Mediterranean Sea (EMS) as a natural laboratory to gain mechanistic understanding of biogeochemical and ecosystem transitions of a future (sub-)tropical ocean affected by global warming and other anthropogenic pressures. The M197 cruise on RV Meteor has the following objectives: (i) characterising nutrient biogeochemistry and phytoplankton nutrient limitation of seawaters in the Eastern Mediterranean Sea, (ii) documenting in detail the microbial communities that inhabit these waters from the surface ocean to sediments, (iii) assessing mechanistic connections between nutrient biogeochemistry, surface ocean productivity, deeper water metabolism, and shelf sediments in the cycling of carbon and major nutrients, (iv) using the sedimentary record to assess past environmental change in the EMS. Data were recorded within the EEZs of Greece and Cyprus. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project and published according to the FAIR principles. These data should not be used for navigational purposes.

Raw water column data were collected aboard RV METEOR during cruise M197 using a Kongsberg EM 710 multibeam echosounder. The expedition took place during 30.12.2023 - 06.02.2024 from Limassol (Republic of Cyprus) to Catania (Italy) in the Mediterranean. The overarching aim was to use the rapidly changing Eastern Mediterranean Sea (EMS) as a natural laboratory to gain mechanistic understanding of biogeochemical and ecosystem transitions of a future (sub-)tropical ocean affected by global warming and other anthropogenic pressures. The M197 cruise on RV Meteor has the following objectives: characterising nutrient biogeochemistry and phytoplankton nutrient limitation of seawaters in the Eastern Mediterranean Sea, (ii) documenting in detail the microbial communities that inhabit these waters from the surface ocean to sediments, (iii) assessing mechanistic connections between nutrient biogeochemistry, surface ocean productivity, deeper water metabolism, and shelf sediments in the cycling of carbon and major nutrients, (iv) using the sedimentary record to assess past environmental change in the EMS. Data were recorded within the EEZs of Greece and Cyprus. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data and the cruise report for details. The data are unprocessed and can therefore contain incorrect depth measurements (artifacts) if not further processed. Note that refraction errors may occur when no proper SVP is applied. Acquisition and provision of the data are part of the DAM Underway Project and published according to the FAIR principles. These data should not be used for navigational purposes.

Abstract Background The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary. Results Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate. Conclusion Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.