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This presentation was delivered at the 2022 Conference "Intelligent Systems for Molecular Biology" in the Bio-Ontologies COSI Track on Wednesday, July 13. Abstract We have recently published an updated genome assembly and annotation of our model organism \Pseudomonas fluorescens SBW25. We are now facing the challenge to keep the annotation up to date with novel results from experimental and computational studies of gene function, fitness assays, regulatory and metabolic networks in a continuous, transparent, and accessible manner. In this contribution we will present how we combine various opensource software tools and open data and metadata standards into a public knowledge base for our model organism. The central part is our genome database and genome browser which is based on the opensource framework Tripal. It allows internal and external colleagues to feed in their data and results in a curated fashion. To further integrate our data we are working on a Linked Data architecture that connects our genome database to various *omics databanks such as UniProt, KEGG or Rfam, as well as to internal datasources such as our microscopy image database, strain database, sequence data repository, and data sharing platform to form an organism specific knowledge graph. By exposing a public SPARQL endpoint, our data ultimately becomes part of the world wide semantic web that incorporates other, domain specific knowledge graphs but also generic data sources such as Wikipedia (via WikiData) and social media hubs. In this way, our system facilitates the growth of the Pseudomonas fluorescens SBW25 knowledge graph both through manual explorations as well as through automated procedures. All components of our system are opensource products. We heavily benefit from open data and metadata standards and we strive to ``pay'' back to the opensource community by contributing customizations to the various software projects and by making our genome annotation ontology part of the public domain.

Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using an in silico model describing the genomes of single-celled asexual organisms that coevolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can promote the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock-paper-scissor dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, which beat streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but improves lineage viability by hindering the proliferation of TEs. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

A major evolutionary transition in individuality, at any level of the biological hierarchy, occurs when groups become capable of participating in Darwinian processes as units of selection. Identifying transitions in individuality can be problematic because apparent selection at one level of the biological hierarchy may be a by-product of selection occurring at another level. Here we discuss various approaches to this ‘levels-of-selection’ problem, drawing attention to the futility of designating traits to hierarchical levels prior to determining the level of selection. While individuals can exhibit traits that are maintained by selection at any level in the biological hierarchy, terms synonymous with ‘collective (group) trait’ or ‘particle trait’ are often applied prematurely. We argue that traits should not be assigned a priori to a hierarchical level, but may respond to selection at different levels depending on environmental conditions. This point is illustrated by an experiment in which groups of the bacterium Pseudomonas fluorescens reproduced via life cycles involving soma- and germline-like phases. The rate of transition between the two cell types was a focus of selection, and might be regarded as a property of groups, cells, or even genes. Philosophical analyses reveal that this trait evolved to be higher in one treatment as a result of its emergent relation to group fitness (contributing to the evolution of individuality), and lower in another treatment because of cell-level selection. An a priori designation of transition rate as either a ‘group trait’ or a ‘cell trait’ may have masked the true level of selection.