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The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.

The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the “Tuberculosis-Simiae,” “Terrae,” “Triviale,” “Fortuitum-Vaccae,” and “Abscessus-Chelonae” clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the “Abscessus-Chelonae” clade forms the deepest branching lineage and does not form a monophyletic grouping with the “Fortuitum-Vaccae” clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the “Tuberculosis-Simiae” clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the “Fortuitum-Vaccae,” “Terrae,” “Triviale,” and “Abscessus-Chelonae” clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.

Genome sequences are making available an unprecedented amount of genetic information that has the potential to reliably elucidate many aspects of physiology, biochemistry, and evolutionary relationships of different organisms. For efficient analyses of the vast amount of genomic sequence data, new reductive approaches are needed which can identify reliable genetic characteristics that are specific for either particular species or related groups of organisms. These characteristics provide novel means for distinguishing different organisms and for understanding their evolutionary history as well as novel tools for phenotypic, behavioral, and biochemical studies. The papers collected in this research topic discuss the application of comparative genomic techniques in a wide range of modalities covering the evolution, classification, identification, and characterization of bacteria and viruses. The evolutionary relationships of bacterial organisms form the underlying basis of their classification. Koton et al. utilize genomic sequence data to elucidate the evolutionary interrelationships of Vibrio vulnificus strains and to both trace the origin and identify unique genomic characteristics of V. vulnificus biotype 3. The comparative genomic analyses completed by Koton et al. are a model of how to utilize the comparative analysis of core, accessory, and unique genomic elements in order to understand the interrelationships of various strains of a single bacterial species. Bacterial classification at the genus and species level, however, is highly structured and often based on the characterization of a limited number of strains (often a single isolate) focussed on the 16S rRNA gene and a number of phenotypic and chemotaxonomic properties (Tindall et al., 2010). Sutcliffe argues that the current standards for classification have limited utility, are time consuming to perform, and are inadequate to face the exponentially growing number bacterial isolates being discovered. He suggests that future classification should focus on utilizing genome sequence data and genome derived characteristics in order to define and delineate bacterial groups. Sawana et al. provide a practical example of this type of genome-centric classification. In their study they utilize genome sequence data to identify multiple highly specific molecular signatures or characteristics which differentiate two main groups within the large and diverse genus Burkholderia. They then divide the genus Burkholderia into two genera based on these genome-derived characteristics (viz. Burkholderia and Paraburkholderia). This group of researchers has previously applied similar techniques to divide the genus Borrelia into two genera, Borrelia and Borreliella (Adeolu and Gupta, 2014), and the genus Thermotoga into two genera, Thermotoga and Pseudothermotoga (Bhandari and Gupta, 2014). The benefits of basing classification on genome sequence analysis are numerous. Firstly, genome sequence data is more easily and consistently comparable between different organisms than phenotypic or chemotaxonomic properties which allows for more reliable and consistent delineation between organisms. Secondly, genetic and molecular characteristics universally shared by a defined group of organisms are more stable over time than chemotaxonomic characteristics and are unique to the group for which they were identified facilitating their use in the identification and classification of novel members of the group. Lastly, the identified genomic and molecular differences form the basis of any recognized or unrecognized phenotypic or biochemical differences between the different groups of organisms, thus, they are important novel targets of study and should lead to a greater focus on understanding of the underlying biological differences between the indicated groups. The utility of comparative genomic analysis in studying the underlying biological differences between groups of organisms is exemplified by Yang et al. who utilize the comparative analysis of Microcystis aeruginosa genomes to identify the CRISPR-Cas systems of different Microcystis aeruginosa subgroups, giving novel insights into their resistance to bacteriophages and their ability to modulate genomic stability and plasticity. Liu et al. utilize a number of biochemical assays to characterize the function of a laterally transferred gene cluster containing the tetR gene, identified via comparative genomic techniques. They show that the tetR gene and TetR protein contribute to cell survival under oxidative stress and are able to identify a number of regulatory roles played by the TetR protein. Taken together, these two studies exemplify the utility of studying and characterizing the genome derived characteristics that are beginning to be used to classify bacterial groups. Viruses and virus-like particles represent the most abundant sources of DNA in the environment (Weinbauer, 2004). Due to the size, plasticity, and unique composition of viral genomes, they represent particularly interesting candidates for comparative analysis. Despite this, viral genome are relatively unexplored in comparison to both eukaryotic and prokaryotic genomes. Chan et al. use genome sequence data to reveal the evolutionary relationships between the members of N4-like phage genus and to define the core genome of all members of the N4-like phage genus and the core genome of the N4-like Roseobacter phages, providing novel insight into the traits which characterize the genus and their evolutionary relationships. Mohiuddin and Schellhorn utilize environmental sampling and comparative genomic analyses of environmental DNA and DNA extracted from virus-like particles to examine the abundance and distribution of different classes of viruses in freshwater environments. These studies both represent useful applications of genomic sequence data and genome derived characteristics to identify and characterize viral groups and populations that are currently underexplored. The papers presented in this research topic exemplify the broad range of applications of comparative genomic analysis and genome derived characteristics in biology and related sciences. The use of genome sequence data to answer novel questions or challenge previously held assumptions is revolutionizing all fields of biology and novel methods and applications of comparative genomics are becoming an indispensable part of modern biological research.

The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.

The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia, and Chlamydiae, along with the Lentisphaerae, Poribacteria, and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, six conserved signature indels (CSIs) in the proteins Cyt c oxidase, UvrD helicase, urease, and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase, and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia, and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae, and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms.