About this Research Topic
As prokaryotic isolate genome and metagenome sequencing become commonplace, the extent of bacterial diversity unravels: entirely new phyla are being discovered, while new genomic diversity within known taxa gradually emerges. This leads to the definition of countless new taxa, delineated on the basis of genomic divergence thresholds. This new standard of taxonomy is now widely accepted but remains arbitrary. To make sense of the diversity observed in natural communities, we still require some insight into the biological and ecological specificities of taxonomic units. A promising approach is the search for ecologically adaptive traits specific to prokaryotic taxa and other phylogenetic groupings using comparative genomics, i.e. a reverse ecology approach.
Being able to recognize taxon-specific adaptations is key to give biological or ecological relevance to taxon labels. Taxon-specific genes and functions may indeed be the reason why an environment is colonized by a given taxon rather than its close relatives. Understanding these selective processes may in turn inform our attempts to predict the evolutionary trajectories of emerging taxa, such as invasive or pathogenic species.
Recent advances in the fine description of prokaryotic pangenomes have shed light on parameters impacting their structure: gene content is primarily driven by the organism’s phylogeny but also by population-scale evolutionary processes and environmental factors. Dense data on within-species diversity are becoming available, allowing the discovery of adaptive genomic features, including traits that are not fixed in the species but differ among subpopulations or fluctuate over time, space, and environments.
The genetic connectivity of prokaryotic organisms via horizontal gene transfer dictates that the structure of pangenomes are investigated at a deeper evolutionary scale, or among sets of organisms we know (or suspect) to be in ecological contact. Analyzing such wide genome samples generates large amounts of data that need modeling, together with isolate source metadata and phenotypes, and accounting for evolutionary processes.
Accordingly, we welcome the contributions of manuscripts related but not limited to the following themes:
• Comparative genomics of prokaryotic taxa or other phylogenetically coherent groups of organisms, as well as combinations of such groups in the light of ecological relatedness
• Pangenome analyses aiming to find key genes (or other genomic features such as sequence variants, large indels, etc.) providing adaptations to their host genome, notably based on synteny breaks, or on phyletic patterns of gene presence/absence/differential frequencies
• Studies analyzing genomic data jointly with high-throughput phenotyping data, multi-omics data, or the composition of natural communities
• Studies using explicit models of genome evolution (e.g. with gene Duplication, Transfer and Loss [DTL]) to map adaptive gene gain/loss events
Keywords: reverse ecology, phylogenetics, comparative genomics, pangenome, genome evolution
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