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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

IEA Wind Task 49: Reference Site Conditions for Floating Wind Arrays

The commercial-scale deployment of floating offshore wind (FOW) projects is expected to take place in a diverse range of sites that may differ significantly from existing fixed-bottom projects. FOW farms are particularly sensitive to the water depth and the meteorological and oceanographic (metocean) and geotechnical conditions at the project site due to the wave-induced system motions and loads as well as the anchoring system constraints imposed by the seafloor conditions. Uncertainty around the site conditions will permeate through all aspects of project design, leading to suboptimal and overly conservative designs, increased costs, and adversely affected performance. As FOW expands into a global industry, metocean and geotechnical conditions will increasingly vary for projects located in different geographic regions or in far-from-shore, deep-water sites. This study represents the outputs of work package 1 of International Energy Agency Wind Task 49, which focuses on the integrated design of floating wind arrays. The primary goal of this study is to establish the type of parameters and constraints required to characterize FOW array reference sites; provide a realistic and publicly available set of reference site conditions to the FOW community as a baseline set of data for individual research projects; identify and categorize any critical gaps in the existing data or methodologies required to define reference site characteristics; and inform and support the design of reference FOW arrays. A building block concept was developed for synthesizing reference sites for the design of FOW arrays. The building blocks include three classes of site conditions focusing on the techno-economic design of FOW projects: metocean conditions, seabed conditions, and coastal infrastructure. All reference site data produced and collected in this study are publicly available.

17 WIND ENERGY↗
DOE OSTI2024

The DUNE Far Detector Vertical Drift Technology. Technical Design Report

DUNE is an international experiment dedicated to addressing some of the questions at the forefront of particle physics and astrophysics, including the mystifying preponderance of matter over antimatter in the early universe. The dual-site experiment will employ an intense neutrino beam focused on a near and a far detector as it aims to determine the neutrino mass hierarchy and to make high-precision measurements of the PMNS matrix parameters, including the CP-violating phase. It will also stand ready to observe supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector implements liquid argon time-projection chamber (LArTPC) technology, and combines the many tens-of-kiloton fiducial mass necessary for rare event searches with the sub-centimeter spatial resolution required to image those events with high precision. The addition of a photon detection system enhances physics capabilities for all DUNE physics drivers and opens prospects for further physics explorations. Given its size, the far detector will be implemented as a set of modules, with LArTPC designs that differ from one another as newer technologies arise. In the vertical drift LArTPC design, a horizontal cathode bisects the detector, creating two stacked drift volumes in which ionization charges drift towards anodes at either the top or bottom. The anodes are composed of perforated PCB layers with conductive strips, enabling reconstruction in 3D. Light-trap-style photon detection modules are placed both on the cryostat's side walls and on the central cathode where they are optically powered. This Technical Design Report describes in detail the technical implementations of each subsystem of this LArTPC that, together with the other far detector modules and the near detector, will enable DUNE to achieve its physics goals.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

DUNE Phase II: scientific opportunities, detector concepts, technological solutions

The international collaboration designing and constructing the Deep Underground Neutrino Experiment (DUNE) at the Long-Baseline Neutrino Facility (LBNF) has developed a two-phase strategy toward the implementation of this leading-edge, large-scale science project. The 2023 report of the US Particle Physics Project Prioritization Panel (P5) reaffirmed this vision and strongly endorsed DUNE Phase I and Phase II, as did the European Strategy for Particle Physics. While the construction of the DUNE Phase I is well underway, this White Paper focuses on DUNE Phase II planning. DUNE Phase-II consists of a third and fourth far detector (FD) module, an upgraded near detector complex, and an enhanced 2.1 MW beam. The fourth FD module is conceived as a “Module of Opportunity”, aimed at expanding the physics opportunities, in addition to supporting the core DUNE science program, with more advanced technologies. This document highlights the increased science opportunities offered by the DUNE Phase II near and far detectors, including long-baseline neutrino oscillation physics, neutrino astrophysics, and physics beyond the standard model. It describes the DUNE Phase II near and far detector technologies and detector design concepts that are currently under consideration. A summary of key R&D goals and prototyping phases needed to realize the Phase II detector technical designs is also provided. DUNE's Phase II detectors, along with the increased beam power, will complete the full scope of DUNE, enabling a multi-decadal program of groundbreaking science with neutrinos.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Research and development of hydrogen carrier based solutions for hydrogen compression and storage

Industrial and public interest in hydrogen technologies has risen strongly recently, as hydrogen is the ideal means for medium to long term energy storage, transport and usage in combination with renewable and green energy supply. In a future energy system, the production, storage and usage of green hydrogen is a key technology. Hydrogen is and will in future be even more used for industrial production processes as a reduction agent or for the production of synthetic hydrocarbons, especially in the chemical industry and in refineries. Under certain conditions material based systems for hydrogen storage and compression offer advantages over the classical systems based on gaseous or liquid hydrogen. This includes in particular lower maintenance costs, higher reliability and safety. Hydrogen storage is possible at pressures and temperatures much closer to ambient conditions. Hydrogen compression is possible without any moving parts and only by using waste heat. In this paper, we summarize the newest developments of hydrogen carriers for storage and compression and in addition, give an overview of the different research activities in this field.

08 HYDROGEN↗
DOE OSTI2020

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO 2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Joint galaxy–galaxy lensing and clustering constraints on galaxy formation

ABSTRACT We compare predictions for galaxy–galaxy lensing profiles and clustering from the Henriques et al. public version of the Munich semi-analytical model (SAM) of galaxy formation and the IllustrisTNG suite, primarily TNG300, with observations from KiDS + GAMA and SDSS-DR7 using four different selection functions for the lenses (stellar mass, stellar mass and group membership, stellar mass and isolation criteria, and stellar mass and colour). We find that this version of the SAM does not agree well with the current data for stellar mass-only lenses with $M_\ast \gt 10^{11}\, \mathrm{ M}_\odot$. By decreasing the merger time for satellite galaxies as well as reducing the radio-mode active galactic nucleus accretion efficiency in the SAM, we obtain better agreement, both for the lensing and the clustering, at the high-mass end. We show that the new model is consistent with the signals for central galaxies presented in Velliscig et al. Turning to the hydrodynamical simulation, TNG300 produces good lensing predictions, both for stellar mass-only (χ2 = 1.81 compared to χ2 = 7.79 for the SAM) and locally brightest galaxy samples (χ2 = 3.80 compared to χ2 = 5.01). With added dust corrections to the colours it matches the SDSS clustering signal well for red low-mass galaxies. We find that both the SAMs and TNG300 predict $\sim 50\, {{\ \rm per\ cent}}$ excessive lensing signals for intermediate-mass red galaxies with 10.2 < log10M*[M⊙] < 11.2 at $r \approx 0.6\, h^{-1}\, \text{Mpc}$, which require further theoretical development.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Stellar and weak lensing profiles of massive galaxies in the Hyper-Suprime Cam survey and in hydrodynamic simulations

ABSTRACT We perform a consistent comparison of the mass and mass profiles of massive (M⋆ > 1011.4 M⊙) central galaxies at z ∼ 0.4 from deep Hyper Suprime-Cam (HSC) observations and from the Illustris, TNG100, and Ponos simulations. Weak lensing measurements from HSC enable measurements at fixed halo mass and provide constraints on the strength and impact of feedback at different halo mass scales. We compare the stellar mass function (SMF) and the Stellar-to-Halo Mass Relation (SHMR) at various radii and show that the radius at which the comparison is performed is important. In general, Illustris and TNG100 display steeper values of α where $M_{\star } \propto M_{\rm vir}^{\alpha }$. These differences are more pronounced for Illustris than for TNG100 and in the inner rather than outer regions of galaxies. Differences in the inner regions may suggest that TNG100 is too efficient at quenching in situ star formation at Mvir ≃ 1013 M⊙ but not efficient enough at Mvir ≃ 1014 M⊙. The outer stellar masses are in excellent agreement with our observations at Mvir ≃ 1013 M⊙, but both Illustris and TNG100 display excess outer mass as Mvir ≃ 1014 M⊙ (by ∼0.25 and ∼0.12 dex, respectively). We argue that reducing stellar growth at early times in $M_\star \sim 10^{9-10} \, \mathrm{M}_{\odot }$ galaxies would help to prevent excess ex-situ growth at this mass scale. The Ponos simulations do not implement AGN feedback and display an excess mass of ∼0.5 dex at r < 30 kpc compared to HSC which is indicative of overcooling and excess star formation in the central regions. The comparison of the inner profiles of Ponos and HSC suggests that the physical scale over which the central AGN limits star formation is r ≲ 20 kpc. Joint comparisons between weak lensing and galaxy stellar profiles are a direct test of whether simulations build and deposit galaxy mass in the correct dark matter haloes and thereby provide powerful constraints on the physics of feedback and galaxy growth. Our galaxy and weak lensing profiles are publicly available to facilitate comparisons with other simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Extensions to models of the galaxy–halo connection

ABSTRACT We explore two widely used empirical models for the galaxy–halo connection, subhalo abundance matching (SHAM) and the halo occupation distribution (HOD), and compare them with the hydrodynamical simulation IllustrisTNG (TNG) for multiple statistics quantifying the galaxy distribution at $n_{\rm gal}\approx 1.3\times 10^{-3}\, ({\rm Mpc}\,h^{-1})^{-3}$. We observe that in their most straightforward implementations, both models fail to reproduce the two-point clustering measured in TNG. We find that SHAM models that use the relaxation velocity, Vrelax, and the peak velocity, Vpeak, perform best, and match the clustering reasonably well, although neither captures adequately the one-halo clustering. Splitting the total sample into sub-populations, we discover that SHAM overpredicts the clustering of high-mass, blue, star-forming, and late-forming galaxies and underpredicts that of low-mass, red, quiescent, and early-forming galaxies. We also study various baryonic effects, finding that subhaloes in the dark-matter-only simulation have consistently higher values of their SHAM-proxy properties than their full-physics counterparts. We then consider a 2D implementation of the HOD model augmented with a secondary parameter (environment, velocity anisotropy, σ2Rhalf-mass, and total potential) tuned so as to match the two-point clustering of the IllustrisTNG galaxies on large scales. We analyse these galaxy populations adopting alternative statistical tools such as galaxy–galaxy lensing, void–galaxy cross-correlations, and cumulants of the density field, finding that the hydrodynamical galaxy distribution disfavours σ2Rhalf-mass and the total potential as secondary parameters, while the environment and velocity anisotropy samples are consistent with full physics across all statistical probes examined. Our results demonstrate the power of examining multiple statistics for determining the secondary parameters that are vital for understanding the galaxy–halo connection.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Limitations to the ‘basic’ HOD model and beyond

ABSTRACT We use the IllustrisTNG cosmological, hydrodynamical simulations to test fundamental assumptions of the mass-based halo occupation distribution (HOD) approach to modelling the galaxy–halo connection. By comparing the clustering of galaxies measured in the 300 Mpc TNG box (TNG300) with that predicted by the standard (basic) HOD model, we find that, on average, the ‘basic’ HOD model underpredicts the real-space correlation function in the TNG300 box by ∼15 per cent on scales of $1 \,\,\lt\,\, r \,\,\lt\,\, 20 \ {\rm Mpc}\, h^{-1}$, which is well beyond the target precision demanded of next-generation galaxy redshift surveys. We perform several tests to establish the robustness of our findings to systematic effects, including the effect of finite box size and the choice of halo finder. In our exploration of ‘secondary’ parameters with which to augment the ‘basic’ HOD, we find that the local environment of the halo, the velocity dispersion anisotropy, β, and the product of the half-mass radius and the velocity dispersion, σ2Rhalfmass, are the three most effective measures of assembly bias that help reconcile the ‘basic’ HOD-predicted clustering with that in TNG300. In addition, we test other halo properties such as halo spin, formation epoch, and halo concentration. We also find that at fixed halo mass, galaxies in one type of environment cluster differently from galaxies in another. We demonstrate that a more complete model of the galaxy–halo connection can be constructed if we combine both mass and local environment information about the halo.

42 ENGINEERING↗
DOE OSTI2021

Galaxy assembly bias and large-scale distribution: a comparison between IllustrisTNG and a semi-analytic model

In this work, we compare large scale structure observables for stellar mass selected samples at z = 0, as predicted by two galaxy models, the hydrodynamical simulation IllustrisTNG and the Santa-Cruz semi-analytic model (SC-SAM). Although both models have been independently calibrated to match observations, rather than each other, we find good agreement between the two models for two-point clustering and galaxy assembly bias signatures. The models also show a qualitatively similar response of occupancy and clustering to secondary halo parameters other than mass, such as formation history and concentration, although with some quantitative differences. Thus, our results demonstrate that the galaxy–halo relationships in SC-SAM and TNG are quite similar to first order. However, we also find areas in which the models differ. For example, we note a strong correlation between halo gas content and environment in TNG, which is lacking in the SC-SAM, as well as differences in the occupancy predictions for low-mass haloes. Moreover, we show that higher order statistics, such as cumulants of the density field, help us to accurately describe the galaxy distribution and discriminate between models that show degenerate behaviour for two-point statistics. Our results suggest that SAMs are a promising cost-effective and intuitive method for generating mock catalogues for next generation cosmological surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

H α emission in local galaxies: star formation, time variability, and the diffuse ionized gas

ABSTRACT The nebular recombination line H α is widely used as a star formation rate (SFR) indicator in the local and high-redshift Universe. We present a detailed H α radiative transfer study of high-resolution isolated Milky-Way and Large Magellanic Cloud simulations that include radiative transfer, non-equilibrium thermochemistry, and dust evolution. We focus on the spatial morphology and temporal variability of the H α emission, and its connection to the underlying gas and star formation properties. The H α and H β radial and vertical surface brightness profiles are in excellent agreement with observations of nearby galaxies. We find that the fraction of H α emission from collisional excitation amounts to fcol ∼ 5–$10{{\ \rm per\ cent}}$, only weakly dependent on radius and vertical height, and that scattering boosts the H α luminosity by $\sim 40{{\ \rm per\ cent}}$. The dust correction via the Balmer decrement works well (intrinsic H α emission recoverable within 25 per cent), though the dust attenuation law depends on the amount of attenuation itself both on spatially resolved and integrated scales. Important for the understanding of the H α–SFR connection is the dust and helium absorption of ionizing radiation (Lyman continuum [LyC] photons), which are about $f_{\rm abs}\approx 28{{\ \rm per\ cent}}$ and $f_{\rm He}\approx 9{{\ \rm per\ cent}}$, respectively. Together with an escape fraction of $f_{\rm esc}\approx 6{{\ \rm per\ cent}}$, this reduces the available budget for hydrogen line emission by nearly half ($f_{\rm H}\approx 57{{\ \rm per\ cent}}$). We discuss the impact of the diffuse ionized gas, showing – among other things – that the extraplanar H α emission is powered by LyC photons escaping the disc. Future applications of this framework to cosmological (zoom-in) simulations will assist in the interpretation of spectroscopy of high-redshift galaxies with the upcoming James Webb Space Telescope.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

The first quiescent galaxies in TNG300

We identify the first quiescent galaxies in TNG300, the largest volume of the IllustrisTNG cosmological simulation suite, and explore their quenching processes and time evolution to z = 0. We find that the first quiescent galaxies with stellar masses M_* > 3 × 10^10 M_⊙ and specific star formation rates sSFR < 10^−11 yr^−1 emerge at z ∼ 4.2 in TNG300. Suppression of star formation in these galaxies begins with a thermal mode of active galactic nucleus feedback at z ∼ 6, and a kinetic feedback mode acts in each galaxy by z ∼ 4.7 to complete the quenching process, which occurs on a time-scale of ∼0.35 Gyr. Surprisingly, we find that the majority of these galaxies are not the main progenitors of their z = 0 descendants; instead, four of the five galaxies fall into more massive galaxies in subsequent mergers at a range of redshifts 2.5 < z < 0.2. By z = 0, these descendants are the centres of galaxy clusters with average stellar masses of 8 × 10^11 M_⊙. We make predictions for the first quenched galaxies to be located by the JWST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Interpreting Sunyaev–Zel’dovich observations with MillenniumTNG: mass and environment scaling relations

ABSTRACT Sunyaev–Zel’dovich (SZ) measurements can dramatically improve our understanding of the intergalactic medium and the role of feedback processes in galaxy formation, allowing us to calibrate important astrophysical systematics in cosmological constraints from weak lensing galaxy clustering surveys. However, the signal is only measured in a two-dimensional projection, and its correct interpretation relies on understanding the connection between observable quantities and the underlying intrinsic properties of the gas, in addition to the relation between the gas and the underlying matter distribution. One way to address these challenges is through the use of hydrodynamical simulations such as the high-resolution, large-volume MillenniumTNG suite. We find that measurements of the optical depth, τ, and the Compton-y parameter, Y, receive large line-of-sight contributions that can be removed effectively by applying a compensated aperture photometry filter. In contrast with other τ probes (e.g. X-rays and fast radio bursts), the kinematic SZ-inferred τ receives most of its signal from a confined cylindrical region around the halo due to the velocity decorrelation along the line of sight. Additionally, we perform fits to the Y–M and τ–M scaling relations and report best-fitting parameters adopting the smoothly broken power law formalism. We note that subgrid physics modelling can broaden the error bar on these by 30 per cent for intermediate-mass haloes (${\sim }10^{13} \, {\rm M}_{\odot }$). The scatter of the scaling relations can be captured by an intrinsic dependence on concentration and an extrinsic dependence on tidal shear. Finally, we comment on the effect of using galaxies rather than haloes in observations, which can bias the inferred profiles by ∼20 per cent for L* galaxies.

Hadzhiyska, Boryana (ORCID:0000000223123121)↗
DOE OSTI2023

Cosmological structure formation and soliton phase transition in fuzzy dark matter with axion self-interactions

Herein we investigate cosmological structure formation in fuzzy dark matter (FDM) with the attractive self-interaction (SI) with numerical simulations. Such a SI would arise if the FDM boson were an ultra-light axion, which has a strong CP symmetry-breaking scale (decay constant). Although weak, the attractive SI may be strong enough to counteract the quantum ‘pressure’ and alter structure formation. We find in our simulations that the SI can enhance small-scale structure formation, and soliton cores above a critical mass undergo a phase transition, transforming from dilute to dense solitons.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase γ

Abstract The mitochondrial single-stranded DNA (ssDNA) binding protein, mtSSB or SSBP1, binds to ssDNA to prevent secondary structures of DNA that could impede downstream replication or repair processes. Clinical mutations in the SSBP1 gene have been linked to a range of mitochondrial disorders affecting nearly all organs and systems. Yet, the molecular determinants governing the interaction between mtSSB and ssDNA have remained elusive. Similarly, the structural interaction between mtSSB and other replisome components, such as the mitochondrial DNA polymerase, Polγ, has been minimally explored. Here, we determined a 1.9-Å X-ray crystallography structure of the human mtSSB bound to ssDNA. This structure uncovered two distinct DNA binding sites, a low-affinity site and a high-affinity site, confirmed through site-directed mutagenesis. The high-affinity binding site encompasses a clinically relevant residue, R38, and a highly conserved DNA base stacking residue, W84. Employing cryo-electron microscopy, we confirmed the tetrameric assembly in solution and capture its interaction with Polγ. Finally, we derived a model depicting modes of ssDNA wrapping around mtSSB and a region within Polγ that mtSSB binds.

Biochemistry & Molecular Biology↗
DOE OSTI2024

DNA double-strand break movement in heterochromatin depends on the histone acetyltransferase dGcn5

Abstract Cells employ diverse strategies to repair double-strand breaks (DSBs), a dangerous form of DNA damage that threatens genome integrity. Eukaryotic nuclei consist of different chromatin environments, each displaying distinct molecular and biophysical properties that can significantly influence the DSB-repair process. DSBs arising in the compact and silenced heterochromatin domains have been found to move to the heterochromatin periphery in mouse and Drosophila to prevent aberrant recombination events. However, it is poorly understood how chromatin components, such as histone post-translational modifications, contribute to these DSB movements within heterochromatin. Using irradiation as well as locus-specific DSB induction in Drosophila tissues and cultured cells, we find enrichment of histone H3 lysine 9 acetylation (H3K9ac) at DSBs in heterochromatin but not euchromatin. We find this increase is mediated by the histone acetyltransferase dGcn5, which rapidly localizes to heterochromatic DSBs. Moreover, we demonstrate that in the absence of dGcn5, heterochromatic DSBs display impaired recruitment of the SUMO E3 ligase Nse2/Qjt and fail to relocate to the heterochromatin periphery to complete repair. In summary, our results reveal a previously unidentified role for dGcn5 and H3K9ac in heterochromatic DSB repair and underscore the importance of differential chromatin responses at heterochromatic and euchromatic DSBs to promote safe repair.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Transcriptomic Analysis Reveals Novel Regulators of the Scots Pine Stilbene Pathway

Stilbenes accumulate in Scots pine heartwood where they have important roles in protecting wood from decaying fungi. They are also part of active defense responses, and their production is induced by different (a)biotic stressors. The specific transcriptional regulators as well as the enzyme responsible for activating the stilbene precursor cinnamate in the pathway are still unknown. UV-C radiation was the first discovered artificial stress activator of the pathway. Here, we describe a large-scale transcriptomic analysis of pine needles in response to UV-C and treatment with translational inhibitors, both activating the transcription of stilbene pathway genes. We used the data to identify putative candidates for the missing CoA ligase and for pathway regulators. We further showed that the pathway is transcriptionally activated by phosphatase inhibitor, ethylene and jasmonate treatments, as in grapevine, and that the stilbene synthase promoter retains its inducibility in some of the tested conditions in Arabidopsis, a species that normally does not synthesize stilbenes. Shared features between gymnosperm and angiosperm regulation and partially retained inducibility in Arabidopsis suggest that pathway regulation occurs not only via ancient stress-response pathway(s) but also via species-specific regulators. Understanding which genes control the biosynthesis of stilbenes in Scots pine aids breeding of more resistant trees.

4-Coumarate-CoA ligase↗
DOE OSTI2024

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes, and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement integrating all three data types was made by the recently released GeneMark-ETP. We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS, and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under an assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperforms BRAKER1 and BRAKER2. The average transcript-level F1-score is increased by about 20 percentage points on average, whereas the difference is most pronounced for species with large and complex genomes. BRAKER3 also outperforms other existing tools, MAKER2, Funannotate, and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.

59 BASIC BIOLOGICAL SCIENCES↗