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opencc-by-4.0Dec 2022View details →

On the Role of Sub-Grid Variability and Microphysics in Km-Scale Simulations of Mixed-Phase Clouds during Cold Air Outbreaks

Model output data used in manuscript "On the Role of Sub-Grid Variability and Microphysics in Km-Scale Simulations of Mixed-Phase Clouds during Cold Air Outbreaks" currently under review in Journal of Geophysical Research - Atmosphere.

opencc-by-4.0Dec 2022View details →

Input and Output dataset for "Robustness tests for an optical time scale"

The uploaded dataset includes the data reported in the figures of the pubblication Robustness tests for an optical time scale (V Formichella et al 2022 Metrologia 59 015002, DOI 10.1088/1681-7575/ac3801, Euramet Pubblication REPRef-2989)

Data from: Interspecific allometric scaling in eDNA production among Northwestern Atlantic bony fishes reflects physiological allometric scaling

Relating environmental DNA (eDNA) signal strength to organism abundance requires a fundamental understanding of eDNA production. A number of studies have demonstrated that eDNA production may scale allometrically – that is, larger organisms tend to exhibit lower mass-specific eDNA production rates, likely due to allometric scaling in key processes related to eDNA production (e.g. surface area, excretion/egestion). While most previous studies have examined intra-specific allometry, physiological rates and organism surface area also scale allometrically across species. We therefore hypothesize that eDNA production will similarly exhibit inter-specific allometric scaling. To evaluate this hypothesis, we reanalyzed previously published eDNA data from Stoeckle et al. (2021) which compared metabarcoding read count to organism count and biomass data obtained from trawl surveys off the New Jersey coast. Using a Bayesian model we empirically estimated the value of the allometric scaling coefficient ('b') for Northwestern Atlantic bony fishes to be 0.77 (credible interval = 0.64 – 0.92), although our model failed to converge for Chondrichthyan species. We found that integrating allometry significantly improved correlations between organism abundance and metabarcoding read count relative to traditional metrics of abundance (density and biomass) for bony fishes. Although substantial unexplained variation remains in the relationship between read count and organism abundance, our study provides evidence that eDNA production may scale allometrically across species in some contexts. Future studies investigating the relationship between eDNA signal strength and metrics of fish abundance could potentially be improved by accounting for allometry; to this end, we developed an online tool that can facilitate the integration of allometry in eDNA/abundance relationships.

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in the early stages of development. This dataset contains the raw data associated with the statistics and figures reported in an accompanying paper which describes the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community.

Behavioral responses of a large, heat-sensitive mammal to climatic variation at multiple spatial scales

1. Climate warming creates energetic challenges for endothermic species by increasing metabolic and hydric costs of thermoregulation. Although endotherms can invoke an array of behavioral and physiological strategies for maintaining homeostasis, the relative effectiveness of those strategies in a climate that is becoming both warmer and drier is not well understood. 2. In accordance with the heat dissipation limit theory, which suggests that allocation of energy to growth and reproduction by endotherms is constrained by the ability to dissipate heat, we expected that patterns of habitat use by large, heat-sensitive mammals across multiple scales are critical for behavioral thermoregulation during periods of potential heat stress and that they must invest a large portion of time to maintain heat balance. 3. To test our predictions, we evaluated mechanisms underpinning the effectiveness of bed sites for ameliorating daytime heat loads and potential heat stress across the landscape while accounting for other factors known to affect behavior. We integrated detailed data on microclimate and animal attributes of moose Alces alces, into a biophysical model to quantify costs of thermoregulation at fine and coarse spatial scales. 4. During summer, moose spent an average of 67.8% of daylight hours bedded, and selected bed sites and home ranges that reduced risk of experiencing heat stress. For most of the day, shade could effectively mitigate the risk of experiencing heat stress up to 10°C, but at warmer temperatures (up to 20℃) wet soil was necessary to maintain homeostasis via conductive heat loss. Consistent selection across spatial scales for locations that reduced heat load underscores the importance of the thermal environment as a driver of behavior in this heat-sensitive mammal. 5. Moose in North America have long been characterized as riparian-obligate species because of their dependence on woody plant species for food. Nevertheless, the importance of dissipating endogenous heat loads conductively through wet soil suggests riparian habitats also are critical thermal refuges for moose. Such refuges may be especially important in the face of a warming climate in which both high environmental temperatures and drier conditions will likely exacerbate limits to heat dissipation, especially for large, heat-sensitive animals.

Landscape-scale dynamics of a threatened species respond to local-scale conservation management

Landscape-scale approaches are increasingly advocated for species conservation but ensuring landscape level persistence by enlarging the size of patches or increasing their physical connectivity is often impractical. Here, we test how such barriers can be overcome by management of habitat at the local (site-based) level, using a rare butterfly as an exemplar. We used four surveys of the entire UK distribution of the Lulworth Skipper (Thymelicus acteon) over 40 years to test how local habitat influences population density and colonization / extinction dynamics, and parameterized, validated and applied a metapopulation model to simulate effects of varying local habitat quality on regional persistence. We found the total number of populations in four distribution snapshots between 1978 and 2017 varied between 59–84, and from 1997 to 2017, 34% of local populations showed turnover (colonization or extinction). Population density was closely linked to vegetation characteristics indicative of management, namely height and food plant frequency, both of which changed through time. Simulating effects of habitat quality on metapopulation dynamics 40 years into the future suggests coordinated changes to two key components of quality (vegetation height and food plant frequency) would increase patch occupancy above the range observed in the past 40 years (50–80%). In contrast, deterioration of either component below threshold levels leads to metapopulation retraction to core sub-networks of patches, or eventual extirpation. Our results indicate that changes to habitat quality can overcome constraints imposed by habitat patch area and spatial location on relative rates of colonization and local extinction, demonstrating the sensitivity of regional dynamics to targeted in situ management. Local habitat management therefore plays a key role in landscape-scale conservation. Monitoring of population density, and the monitoring and management of local (site-level) habitat quality, therefore represent effective and important components of conservation strategies in fragmented landscapes.

NDVI-based monitoring of long-term vegetation dynamics and responses to multi-time scales droughts in Inner Mongolia

The characteristics of vegetation and drought for different seasons between 1982 and 2015 in Inner Mongolia were studied based on the Normalized Difference Vegetation Index (NDVI) and the Standardized Precipitation Evapotranspiration Index (SPEI). The response of vegetation to drought over various time scales for different seasons and vegetation types was investigated using the maximum Pearson correlation, allowing a discussion about the possible causes of any changes. The results indicate that the vegetation NDVI in Inner Mongolia showed an increasing trend in different seasons, with spring vegetation NDVI (April to May) having the largest significant increasing rate, followed by the growing season (April to October), autumn (September to October), and summer (June to August). Accordingly, the proportion of stations with decreasing SPEI was, in descending order, summer, growing season, autumn, and spring. Additionally, the magnitude of the SPEI decrease was greater in eastern Inner Mongolia. NDVI and SPEI were positively correlated in most regions of Inner Mongolia, indicating that changes in vegetation in most parts of this region were affected by the spatial and temporal characteristics of drought, the correlation being them being strongest in the growing season, followed by summer, then spring and autumn. Considering the different types of vegetation, forests were less affected by drought, with broadleaf forests more affected than coniferous forests. The meadow steppes and typical steppes were more affected by 12-month droughts in the growing season and summer, 6-month droughts in spring, and 3-month droughts in autumn, with desert steppes mainly affected by 3-month droughts. The shrubs, sandy vegetation, and cropland were mostly affected by droughts in summer, and show a greater response to 3-month droughts in autumn. Finally, the water balance was found to be the most important factor affecting the response of vegetation to drought in Inner Mongolia.

opencc-by-4.0Dec 2022View details →

Exploring the Effects of LC Parameters on Retention Indices of Small Molecules using Amine Scaling - Supplementary Data

In this document the retention times, calculated retention indices and calculated delta retention indices can be found that were used for the thesis on Exploring the Effects of LC Parameters on Retention Indices of Small Molecules using Amine Scaling, as well as the raw-data files of the performed measurements.

Data from "Molecular Mapping of DR Tau's Protoplanetary Disk, Envelope, Outflow, and Large-Scale Spiral Arm"

Data associated with Huang et al., 2023, "Molecular Mapping of DR Tau's Protoplanetary Disk, Envelope, Outflow, and Large-Scale Spiral Arm," ApJ, 943, 107 The raw data can be obtained by requesting data from program W20BE (PI: J. Huang) from the NOEMA archive.  Images images.tar: FITS files of image cubes and moment maps as shown in Figs. 2, 3, 5, 9, and 10 (see also finalimagingscript.py) Spectra spectra.tar: ASCII files of spectra shown in Figs. 1 and 9 (see also finalimagingscript.py)  Measurement sets (CASA format) drtau_LINENAME_corrected.ms.tar: Measurement set for a given line, corresponding to drtau_LINENAME_selfcal-contsub.uvt in lines_contsub_uvt.tar  drtau_ui_cont_corrected.ms.tar: Continuum measurement set corresponding to the UI baseband, generated from w20be-ui-cont-selfcal.uvt in continuum_uvt.tar  UV tables (GILDAS format) LR_uvt.tar: Pipeline-calibrated UV tables of low-resolution data (see w20be-tables-LR.clic) HR_uvt.tar: Pipeline-calibrated UV tables of high-resolution data (see w20be-tables-HR.clic) continuum_uvt.tar: Self-calibrated, spectrally averaged continuum UV tables generated from LR_uvt.tar lines_contsub_uvt.tar: Self-calibrated, continuum-subtracted line UV tables generated from the UV tables in HR_uvt.tar Scripts w20be-tables-LR.clic: CLIC script used to output UV tables of low-resolution data from the pipeline-calibrated data (output contained in LR_uvt.tar) w20be-tables-HR.clic: CLIC script used to output UV tables of high-resolution data from the pipeline-calibrated data (output contained in HR_uvt.tar) uvfitstoms.py: Script to export uvfits files to measurement sets and to correct the metadata in the measurement sets  finalimagingscript.py: CASA script used to generate imaging products in images.tar and spectra in spectra.tar  Other: calib.tar: Files output by NOEMA pipeline

Large-scale survey of excitatory synapses reveals sublamina-specific and asymmetric synapse disassembly patterns in a neurodegenerative circuit

Dataset associated with the manuscript titled "Large-scale survey of excitatory synapses reveals sublamina-specific and asymmetric synapse disassembly patterns in a neurodegenerative circuit"

Improving stratocumulus cloud amounts in a 200-m resolution multi-scale modeling framework through tuning of its interior physics Part 2

This dataset includes model outputs averaged from day 2 to day 15 using the multiscale modeling framework (MMF, also referred to as ``superparameterization'') for <ul> <li>Low-resolution MMF (LR): SP_newsst_long_fluxout_L125_ERA5_2008_F-MMF1_frontera_ne16pg2_r05_oQU240_CRM1_32_x_120z1200m.5s_crm_nx_rad_16_np_768_nlev_125.frontera.cam.h0.2008-10_2To15.nc <ul> <li>crm_nx = 32, crm_ny = 1, crm_dx = 1200 m, crm_dt = 5s, crm_nx_rad = 16, crm_ny_rad=1</li> </ul> </li> <li>High-resolution MMF (HR): UP_newsst_long_fluxout_L125_ERA5_2008_F-MMF1_frontera_ne16pg2_r05_oQU240_CRM1_64_x_120z200m.0.5s_crm_nx_rad_16_np_768_nlev_125.frontera.cam.h0.2008-10_2To15.nc <ul> <li>crm_nx = 64, crm_ny = 1, crm_dx = 200 m, crm_dt = 0.5s, crm_nx_rad = 16, crm_ny_rad=1</li> </ul> </li> <li>Same as HR, but considers hyperviscosity with tau = 30s (HRh30): UPhyperlag30_newsst_fluxout_L125_ERA5_2008_F-MMF1_frontera_ne16pg2_r05_oQU240_CRM1_64_x_120z100m.0.5s_crm_nx_rad_16_np_768_nlev_125.frontera.cam.h0.2008-10_2To15.nc</li> <li>Same as HR, but considers hyperviscosity with tau = 150s (HRh15): UPhyperlag15_newsst_fluxout_L125_ERA5_2008_F-MMF1_frontera_ne16pg2_r05_oQU240_CRM1_64_x_120z100m.0.5s_crm_nx_rad_16_np_768_nlev_125.frontera.cam.h0.2008-10_2To15.nc</li> <li>Same as HRh, but considers both hyperviscosity and sedimentation (HRhs15) with tau = 30s and sigmag = 1.5: HPhyper_sedi15_long_newsst_fluxout_L125_ERA5_2008_F-MMF1_frontera_ne16pg2_r05_oQU240_CRM1_64_x_120z200m.0.5s_crm_nx_rad_16_np_768_nlev_125.frontera.cam.h0.2008-10_2To15.nc</li> <li>Same as HRh, but considers both hyperviscosity and sedimentation (HRhs12) with tau = 30s and sigmag = 1.2: HPhyper_sedi12_long_newsst_fluxout_L125_ERA5_2008_F-MMF1_frontera_ne16pg2_r05_oQU240_CRM1_64_x_120z200m.0.5s_crm_nx_rad_16_np_768_nlev_125.frontera.cam.h0.2008-10_2To15.nc</li> </ul>

Data for: Bed-scale impact and recovery of a commercially important intertidal seaweed

As the value of ecosystem-based management (EBM) approaches is increasingly recognized in marine ecosystems, it is critical that the impacts of resource harvest are assessed at various spatial scales. This is particularly true for habitat-forming resources, such as wild seaweeds, that act as foundation species by physically structuring ecosystems. The impacts of spatially heterogeneous harvest may change with scale and have different management implications based on the ecosystem process or organism under consideration. Ascophyllum nodosum (hereafter rockweed) is a canopy-forming fucoid seaweed endemic to rocky coastlines in the North Atlantic Ocean that has been harvested for centuries. We conducted a Before-After Control-Impact study of commercial rockweed harvest at 38 sites across the coast of Maine (USA) from 2018 to 2020 in an effort to understand impact and one-year recovery of two rockweed bed structural characteristics, height and biomass, at a scale similar to a single harvest event. Our results indicate that rockweed harvest is spatially heterogeneous at the scale of the rockweed bed, and as a result, the effect sizes of harvest at this scale are smaller than those reported in previous studies that assessed smaller spatial scales. Mean rockweed biomass recovered to pre-harvest values after one year of recovery, but mean rockweed height remained lower at impacted sites. While post-harvest recovery was generally high in our study, sites that experienced higher intensities of harvest were less likely to fully recover height or biomass one year post-harvest. Our findings provide resource managers with a bed-scale perspective that can inform EBM approaches, particularly for population-level management of harvested resources and impacts of harvest on highly mobile organisms—such as birds and fish—that interact with these ecosystems at larger spatial scales.

Improving stratocumulus cloud amounts in a 200-m resolution multi-scale modeling framework through tuning of its interior physics Part 1

This dataset includes 6-month simulations using the ne30pg2 grid. Monthly averaged output files from six experiments are included. <ul> <li>E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1 <ul> <li>The config options for this control simulation is <pre>CAM_CONFIG_OPTS = -mach summit -phys default -use_MMF -crm samxx -nlev 60 -crm_nz 50 -crm_dt 10 -crm_dx 2000 -crm_nx 64 -crm_ny 1 -crm_nx_rad 4 -crm_ny_rad 1 -rad rrtmgp -rrtmgpxx -MMF_microphysics_scheme sam1mom -chem none -nlev 125 -crm_nz 115 -crm_dt 2 -crm_dx 200 -crm_nx 256 -crm_ny 1 -crm_nx_rad 4 -crm_ny_rad 1 -use_MMF_VT -cppdefs ' -DMMF_ESMT -DMMF_USE_ESMT -DMMF_HYPERVISCOSITY -DMMF_SEDIMENTATION ' </pre> </li> </ul> </li> <li>E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED <ul> <li>The HV.SED control case is the same as the control (E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1), but considered both hyperciscosity and sedimentation processes.</li> </ul> </li> <li>E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED.QW_1E-04 <ul> <li>Same as the HV.SED control case (E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED), but changed the autoconversion thresholds for liquid from QW_1E-03 (default) to QW_1E-04.</li> </ul> </li> <li>E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED.QW_5E-04 <ul> <li>Same as the HV.SED control case (E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED), but changed the autoconversion thresholds for liquid from QW_1E-03 (default) to QW_5E-04.</li> </ul> </li> <li>E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED.QW_5E-04_QI_5E-05 <ul> <li>Same as the HV.SED control case (E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED), but changed the autoconversion thresholds for liquid from QW_1E-03 (default) to QW_1E-04 and ice from QI_1E-04 (default) to QI_5E-05.</li> </ul> </li> <li>E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED.QW_5E-04_QI_8E-05 <ul> <li>Same as the HV.SED control case (E3SM.INCITE2022-LOW-CLD-00.ne30pg2.F2010-MMF1.L125_115.NXY_256x1.HV.SED), but changed the autoconversion thresholds for liquid from QW_1E-03 (default) to QW_1E-04 and ice from QI_1E-04 (default) to QI_8E-05.</li> </ul> </li> </ul>

Dataset for: Indirect nitrous oxide emission factors of fluvial networks can be predicted by dissolved organic carbon and nitrate from local to global scales

Streams and rivers are important sources of nitrous oxide (N2O), a powerful greenhouse gas. Estimating global riverine N2O emissions is critical for the assessment of anthropogenic N2O emission inventories. The indirect N2O emission factor (EF5r) model, one of the bottom-up approaches, adopts a fixed EF5r value to estimate riverine N2O emissions based on IPCC methodology. However, the estimates have considerable uncertainty due to the large spatiotemporal variations in EF5r values. Factors regulating EF5r are poorly understood at the global scale. Here, we combine 4-year in situ observations across rivers of different land use types in China, with a global meta-analysis over six continents, to explore the spatiotemporal variations and controls on EF5r values. Our results show that the EF5r values in China and other regions with high N loads are lower than those for regions with lower N loads. Although the global mean EF5r value is comparable to the IPCC default value, the global EF5r values are highly skewed with large variations, indicating that adopting region-specific EF5r values rather than revising the fixed default value is more appropriate for the estimation of regional and global riverine N2O emissions. The ratio of dissolved organic carbon to nitrate (DOC/NO3-) and NO3- concentration are identified as the dominant predictors of region-specific EF5r values at both regional and global scales because stoichiometry and nutrients strictly regulate denitrification and N2O production efficiency in rivers. A multiple linear regression model using DOC/NO3- and NO3- is proposed to predict region-specific EF5r values. The good fit of the model associated with easily obtained water quality variables allows its widespread application. This study fills a key knowledge gap in predicting region-specific EF5r values at the global scale and provides a pathway to estimate global riverine N2O emissions more accurately based on IPCC methodology. This dataset is a global integrated N2O dataset including data from 4-year (2017-2020) in situ measurements of six large rivers in China, 3-year (2018-2020) in situ measurements of urban river networks in Beijing of China, and 825 measurements from 70 published papers over six continents. The data includes dissolved N2O concentration, biogeochemical (DOC, NO3-, NH4+, temperature, and DO), climatological (climate zones), and geographic (region, location, and land cover) information.

DATA: molecularly enhanced proof of concept for targeting cocrystals at molecular scale in continuous pharmaceuticals cocrystallization - part 2

This is the cleansed files for CoCryM project carried out at the University of Limerick, Ireland for a MSCA postdoctoral fellowship.  Link to PNAS paper <a href="https://www.pnas.org/doi/10.1073/pnas.2114277119">https://www.pnas.org/doi/10.1073/pnas.2114277119</a>  (molecularly enhanced proof of concept for targeting cocrystals at molecular scale in continuous pharmaceuticals cocrystallization)  Original uploaded files on 10 September 2021:  <ol> <li><a href="https://doi.org/10.5281/zenodo.6164838">https://doi.org/10.5281/zenodo.6164838</a></li> <li><a href="https://doi.org/10.5281/zenodo.6189068">https://doi.org/10.5281/zenodo.6189068</a></li> <li><a href="https://doi.org/10.5281/zenodo.6189100">https://doi.org/10.5281/zenodo.6189100</a></li> <li><a href="https://doi.org/10.5281/zenodo.6189715">https://doi.org/10.5281/zenodo.6189715</a></li> <li><a href="https://doi.org/10.5281/zenodo.6189885">https://doi.org/10.5281/zenodo.6189885</a></li> </ol>   Inhouse: https://sites.google.com/view/makhansary/publications

Scaling up gas and electric cooking in low- and middle-income countries: Climate threat or mitigation strategy with co-benefits?

Nearly three billion people in low- and middle-income countries (LMICs) rely on polluting fuels, resulting in millions of avoidable deaths annually. Polluting fuels also emit short-lived climate forcers and greenhouse gases (GHGs). Liquefied petroleum gas (LPG) and grid-based electricity are scalable alternatives to polluting fuels but have raised climate and health concerns. Here, we compare emissions and climate impacts of a business-as-usual household cooking fuel trajectory to four large-scale transitions to gas and/or grid electricity in 77 LMICs. We account for upstream and end-use emissions from gas and electric cooking, assuming electrical grids evolve according to the 2022 World Energy Outlook's "Stated Policies" Scenario. We input the emissions into a reduced-complexity climate model to estimate radiative forcing and temperature changes associated with each scenario. We find full transitions to LPG and/or electricity decrease emissions from both well-mixed GHG and short-lived climate forcers, resulting in a roughly 5 millikelvin global temperature reduction by 2040. Transitions to LPG and/or electricity also reduce annual emissions of PM2.5 by over 6 Mt (99%) by 2040, which would substantially lower health risks from Household Air Pollution.

Dataset to analyze the psychometric and structural properties of a scale designed to measure attitudes to integrated flood risk management

The content of this reference includes the dataset generated by means of a questionnaire survey to a representative sample (N=406) of a city of Zamora (Spain). It contains 39 columns (c) which represents the following variables: Flooding area (c1); Flood risk perception (c2 to c7); Attitudes toward flood mitigation measures (c8 to c22); Perceived efficiency of general flood mitigation measures (c23 to c28); Assessment of the adequacy of overall flood risk management in the city and neighborhood (c29 to c30); Safety, environment, and economy preferences in flood risk management (c31 to c33); Postal code (c34); Age (c35); Age intervals (c36); sex (c37); Factorial saved loadings (c38 to c39).

Appendix of Large-Scale Evaluation of Method-Level Bug Localization with FinerBench4BL

Appendix of "Large-Scale Evaluation of Method-Level Bug Localization with FinerBench4BL"   FinerBench4BL is available at the following URL <a href="https://github.com/salab/FinerBench4BL">https://github.com/salab/FinerBench4BL</a>

Datasets from: Local- and landscape-scale drivers of terrestrial herbaceous plant diversity along a tropical rainfall gradient in Western Ghats, India

This data set contains information on local- and landscape-level terrestrial herbaceous plant diversity and critical abiotic factors along a 36-km East-West transect in Mudumalai Tiger Reserve, Tamil Nadu India. Understory angiosperms with no above-ground wood (secondary cambial growth) were considered as herbaceous plants.

A chromosome-scale high-contiguity genome assembly of the threatened cheetah (Acinonyx jubatus)

The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.