Phylogenomic and comparative analyses on protein sequences from Halobacteria to identify taxon-specific molecular markers which demarcate different Halobacteriaceae and Haloarculaceae genera

Members of the class <i>Halobacteria</i>, due to their widespread distribution in different high-salt environments and potential biotechnological applications, are being discovered at a rapid pace. In recent years, the classification of <i>Halobacteria</i> has undergone major changes, and this class is now divided into 10 families consisting of >77 genera. However, different <i>Halobacteria</i> taxa are presently distinguished based mainly on their branching in phylogenomic trees. No specific characteristics are known which are unique to members of different taxa. To advance our understanding of <i>Halobacteria</i> taxa in this regard, we report here comprehensive phylogenomic and comparative analyses on species from two <i>Halobacteria</i> families, viz. <i>Haloarculaceae</i> and <i>Halobacteriaceae</i>. A phylogenomic tree for 385 <i>Halobacteria</i> species constructed in this work supported the current taxonomy. However, the main objective of this study was to identify molecular markers consisting of conserved signature indels (CSIs) in protein sequences which are uniquely found in the species from the above two families, or those which are specific to their different genera. Our work has identified 105 CSIs in diverse proteins, some of which are specific to <i>Halobacteriaceae</i>, whereas others are exclusively shared characteristics of different <i>Haloarculaceae</i> and <i>Halobacteriaceae</i> genera. Based upon the described CSIs, all genera from these two families containing two or more named species (viz. <i>Halapricum</i>, <i>Halarchaeum</i>, <i>Haloarcula</i>, <i>Halobacterium</i>, <i>Halocatena</i>, <i>Haloglomus</i>, <i>Halomarina</i>, <i>Halomicrobium</i>, <i>Halorarius</i>, <i>Halorhabdus</i>, <i>Halorientalis</i>, <i>Halosegnis</i>, <i>Halosimplex</i>, <i>Halovenus</i> and <i>Natronomonas</i>) can be robustly distinguished from all other <i>Halobacteria</i> genera. The identified CSIs, which are also present in uncharacterized strains of these taxa, provide more definitive means for the demarcation of these <i>Halobacteria</i> taxa and for the identification of new species/strains related to these genera. Because of the predicted functional importance of these CSIs, these taxon-specific molecular markers also provide novel tools for genetic, biochemical and functional studies on these groups of <i>Halobacteria</i>.