Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here we present our largest increase in plant, metazoan and fungal genomes since the project’s inception creating one of the world’s most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We also detail our new efforts in gene annotation, our emerging support for pangenome analysis and efforts to accelerate data dissemination through the Ensembl Rapid Release resource. We also present our new AlphaFold visualisation. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl’s release cycle

A stratospheric prognostic ozone for seamless Earth system models: performance, impacts and future

We have implemented a new stratospheric ozone model in the European Centre for Medium-Range Weather Forecasts (ECMWF) system and tested its performance for different timescales to assess the impact of stratospheric ozone on meteorological fields. We have used the new ozone model to provide prognostic ozone in medium-range and long-range (seasonal) experiments, showing the feasibility of this ozone scheme for a seamless numerical weather prediction (NWP) modelling approach. We find that the stratospheric ozone distribution provided by the new scheme in ECMWF forecast experiments is in very good agreement with observations, even for unusual meteorological conditions such as Arctic stratospheric sudden warmings (SSWs) and Antarctic polar vortex events like the vortex split of year 2002. To assess the impact it has on meteorological variables, we have performed experiments in which the prognostic ozone is interactive with radiation. The new scheme provides a realistic ozone field able to improve the description of the stratosphere in the ECMWF system, as we find clear reductions of biases in the stratospheric forecast temperature. The seasonality of the Southern Hemisphere polar vortex is also significantly improved when using the new ozone model. In medium-range simulations we also find improvements in high-latitude tropospheric winds during the SSW event considered in this study. In long-range simulations, the use of the new ozone model leads to an increase in the correlation of the winter North Atlantic Oscillation (NAO) index with respect to ERA-Interim and an increase in the signal-to-noise ratio over the North Atlantic sector. In our study we show that by improving the description of the stratospheric ozone in the ECMWF system, the stratosphere–troposphere coupling improves. This highlights the potential benefits of this new ozone model to exploit stratospheric sources of predictability and improve weather predictions over Europe on a range of timescales

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project

Toward an improved representation of middle atmospheric dynamics thanks to the ARISE project

This paper reviews recent progress toward understanding the dynamics of the middle atmosphere in the framework of the Atmospheric Dynamics Research InfraStructure in Europe (ARISE) initiative. The middle atmosphere, integrating the stratosphere and mesosphere, is a crucial region which influences tropospheric weather and climate. Enhancing the understanding of middle atmosphere dynamics requires improved measurement of the propagation and breaking of planetary and gravity waves originating in the lowest levels of the atmosphere. Inter-comparison studies have shown large discrepancies between observations and models, especially during unresolved disturbances such as sudden stratospheric warmings for which model accuracy is poorer due to a lack of observational constraints. Correctly predicting the variability of the middle atmosphere can lead to improvements in tropospheric weather forecasts on timescales of weeks to season. The ARISE project integrates different station networks providing observations from ground to the lower thermosphere, including the infrasound system developed for the Comprehensive Nuclear-Test-Ban Treaty verification, the Lidar Network for the Detection of Atmospheric Composition Change, complementary meteor radars, wind radiometers, ionospheric sounders and satellites. This paper presents several examples which show how multi-instrument observations can provide a better description of the vertical dynamics structure of the middle atmosphere, especially during large disturbances such as gravity waves activity and stratospheric warming events. The paper then demonstrates the interest of ARISE data in data assimilation for weather forecasting and re-analyzes the determination of dynamics evolution with climate change and the monitoring of atmospheric extreme events which have an atmospheric signature, such as thunderstorms or volcanic eruptions