# A Genomic Survey of Signalling in the Myxococcaceae
## 1 Introduction  
During the evolution of new species from common ancestors, phenotypic differences often emerge as a result of lineage-specific changes in underlying signalling pathways and regulatory genes. It is therefore important to understand how signalling gene sets change as organisms evolve and to be able to relate those changes to formal taxonomies. Understanding the mutability of signalling gene sets can also provide us with insights into the ecology of contemporary organisms and the molecular mechanisms of their phenotypes. The myxobacteria (order Myxococcus) are renowned for having exceptionally large numbers of signalling genes in their genomes [1; 2; 3]. Particularly common are serine/threonine (Ser/Thr) kinases, which regulate target proteins by reversible phosphorylation, one-component systems (OCSs), which combine a sensory domain with an 'output' response effector domain, and two-component systems (TCSs), which typically comprise a sensor histidine (auto)kinase (HK) which transfers phosphoryl groups to a partner response regulator (RR), sometimes via a phosphotransfer protein (P). Myxobacterial genomes also encode numerous transcription factors (TFs), including DNA-binding transcriptional regulators (TRs), alternative sigma factors and DNA-binding OCSs. In 2015, just twelve myxobacterial genome sequences were publicly available (including three members of family Myxococcae, as currently defined), and analysis of those genomesconfirmed that differences in TCS gene sets scaled with phylogenetic distances between strains [3]. TCS evolution was found to be dominated by gene gain/loss rather than point mutations or intra-gene insertions/deletions [3]. By September 2020, there were 375 myxobacterial genomes available, including 102 from the Myxococcaceae family. Although not as explosive, the last decade also saw an increase in the number of known Myxococcaceae species from 8 [4] to 24, with 14 of the new species identified as a result of genome-led taxonomy [5; 6; 7]. Family Myxococcaceae is dominated by the genera _Coralococcus_ and _Myxococc_ (synonymous with _Pyxidicoccus_), which currently contain ten and twelve species, respectively [7]. The increased availability of genome sequences has allowed pan-genomic analyses of different Myxococcaceae taxa [7; 8; 9]. Such analyses have revealed small core genomes (the genes shared by every member of a taxon). For _Myxococcus xanthus_, only \(\sim\)75% of genes in each genome belong to the core genome, dropping to just 9% of genes when comparing species within the _Myxococcus_ genus [7]. This means that a large proportion of the genes in each myxobacterial genome belong to the accessory pan-genome (genes that are absent from some genomes). Indeed, 63% of the genes constituting the pan-genome of 11 _Myxococcus_ spp. type strains were found to be unique to individual species, presumably having been acquired by lineage-specific duplication (with rapid divergence), or by horizontal transfer [7]. The acquisition of new genes by a genome carries with it the metabolic cost of reproducing those extra genes and consequently results in a fitness disadvantage. The selective advantage of being able to grow faster results in an evolutionary pressure for bacteria to streamline their genomes, rapidly losing genes that do not confer a selective advantage [10]. This pressure to streamline seems to be diminished in the myxobacteria as they possess unusually large genomes, with large accessory genomes [7; 11]. It has been hypothesised that the slow growth exhibited by myxobacteria may result in the reduced pressure to streamline, in turn allowing accumulation of genes that might only occasionally provide a selective advantage [11]. We expected that assessing whether specific genes are part of the core or accessory genome would allow us to distinguish between genes which are functional and contribute to core behaviours/processes, and those which are dispensable: either awaiting loss from the genome, or only beneficial under limited circumstances, or in a subset of taxa.