Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the and Species: Robust Demarcation of Two Family-Level Clades within the Order and Proposal for the Family fam. nov.

Evolutionary relationships amongst and species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera and corresponds to the family whereas another clade, harboring Thermochlorobacter aerophilum, Thermochlorobacteriaceae bacterium GBChlB, and sp. 445, is now proposed as a new family ( fam. nov). In parallel, our comparative genomic analyses have identified 47 conserved signature indels (CSIs) in diverse proteins that are exclusively present in members of the class or its two families, providing reliable means for identification. Two known species in our phylogenomic tree are found to group within a larger clade containing several species and uncultured strains. A CSI in the SecY protein is uniquely shared by the species/strains from this "larger clade". Two additional CSIs, which are commonly shared by species and the "larger clade", support a specific relationship between these two groups. The newly identified molecular markers provide novel tools for genetic and biochemical studies and identification of these organisms.