RAF-like protein kinases mediate a deeply conserved, rapid auxin response.

The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism.

FAIR data station for lightweight metadata management and validation of omics studies.

Background: The life sciences are one of the biggest suppliers of scientific data. Reusing and connecting these data can uncover hidden insights and lead to new concepts. Efficient reuse of these datasets is strongly promoted when they are interlinked with a sufficient amount of machine-actionable metadata.

Systems Biology in ELIXIR: modelling in the spotlight.

In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities.

Comparative Genomics and Physiology of Isolates from Human Intestine Reveal Specialized Mucosal Adaptation.

Akkermansia muciniphila is a champion of mucin degradation in the human gastrointestinal tract. Here, we report the isolation of six novel strains from healthy human donors and their genomic, proteomic and physiological characterization in comparison to the type-strains A. muciniphila MucT and A.

Assembly and Comparison of Neoehrlichia mikurensis Genomes.

Neoehrlichia mikurensis is widely prevalent in across Europe and has been associated with human disease. However, diagnostic modalities are limited, and much is still unknown about its biology. Here, we present the first complete Neoehrlichia mikurensis genomes directly derived from wildlife reservoir host tissues, using both long- and short-read sequencing technologies.

SALARECON connects the Atlantic salmon genome to growth and feed efficiency.

Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species such as salmon.

Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains.

Background: The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype.

Genomic convergence between Akkermansia muciniphila in different mammalian hosts.

Background: Akkermansia muciniphila is a member of the human gut microbiota where it resides in the mucus layer and uses mucin as the sole carbon, nitrogen and energy source. A. muciniphila is the only representative of the Verrucomicrobia phylum in the human gut.

Galactocerebroside biosynthesis pathways of Mycoplasma species: an antigen triggering Guillain-Barré-Stohl syndrome.

Infection by Mycoplasma pneumoniae has been identified as a preceding factor of Guillain-Barré-Stohl syndrome. The Guillain-Barré-Stohl syndrome is triggered by an immune reaction against the major glycolipids and it has been postulated that M. pneumoniae infection triggers this syndrome due to bacterial production of galactocerebroside.

Experimental infrastructure requirements for quantitative research on microbial communities.

Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies.

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes.

To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade.

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses.

Background: Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a "commons.

A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration.

Background: Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hampers production of oxygen sensitive products and drives up costs in large scale fermentation. The inability to perform anaerobic fermentation has been attributed to insufficient ATP production and an inability to produce pyrimidines under these conditions.

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis.

NG-Tax 2.0 is a semantic framework for FAIR high-throughput analysis and classification of marker gene amplicon sequences including bacterial and archaeal 16S ribosomal RNA (rRNA), eukaryotic 18S rRNA and ribosomal intergenic transcribed spacer sequences. It can directly use single or merged reads, paired-end reads and unmerged paired-end reads from long range fragments as input to generate amplicon sequence variants (ASV).

Organohalide-respiring Desulfoluna species isolated from marine environments.

The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1 and D. butyratoxydans MSL71, of which only the former was shown to perform organohalide respiration (OHR).

Metabolic shift induced by synthetic co-cultivation promotes high yield of chain elongated acids from syngas.

Bio-catalytic processes for sustainable production of chemicals and fuels receive increased attention within the concept of circular economy. Strategies to improve these production processes include genetic engineering of bio-catalysts or process technological optimization. Alternatively, synthetic microbial co-cultures can be used to enhance production of chemicals of interest.

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation.

The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain a coherent RDF graph the chosen ontology must be consistently applied. However, addition of new diverse data causes the ontology to evolve, which could lead to accumulation of unintended erroneous composites.

Diversity of tryptophan halogenases in sponges of the genus Aplysina.

Marine sponges are a prolific source of novel enzymes with promising biotechnological potential. Especially halogenases, which are key enzymes in the biosynthesis of brominated and chlorinated secondary metabolites, possess interesting properties towards the production of pharmaceuticals that are often halogenated. In this study we used a polymerase chain reaction (PCR)-based screening to simultaneously examine and compare the richness and diversity of putative tryptophan halogenase protein sequences and bacterial community structures of six Aplysina species from the Mediterranean and Caribbean seas.

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio.

Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesized that Pseudovibrio spp. form mutualistic relationships with their hosts.

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.

Summary: To unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used to process and analyze existing genome annotations. SAPP automatically predicts, tracks and stores structural and functional annotations and associated dataset- and element-wise provenance in a Linked Data format, thereby enabling information mining and retrieval with Semantic Web technologies.

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.

A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method.

Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1.

Haloalkanoates are environmental pollutants that can be degraded aerobically by microorganisms producing hydrolytic dehalogenases. However, there is a lack of information about the anaerobic degradation of haloalkanoates. Genome analysis of AW-1, a facultative anaerobic chlorate-reducing bacterium, showed the presence of two putative haloacid dehalogenase genes, the l-DEX gene and , encoding an l-2-haloacid dehalogenase (l-DEX) and a halocarboxylic acid dehydrogenase (DehI), respectively.