AUTHOR=Gupta Radhey S. , Patel Sudip 

TITLE=Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2020

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.02821

DOI=10.3389/fmicb.2019.02821

ISSN=1664-302X

ABSTRACT=<p>The family <italic>Caryophanaceae</italic>/<italic>Planococcaceae</italic> is a taxonomically heterogeneous assemblage of &gt;100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily <italic>Bacillaceae</italic>, the evolutionary history of this family, containing the potent mosquitocidal species <italic>Lysinibacillus sphaericus</italic>, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family <italic>Caryophanaceae</italic>/<italic>Planococcaceae</italic> and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available <italic>Caryophanaceae</italic>/<italic>Planococcaceae</italic> and representative <italic>Bacillaceae</italic> species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved <italic>Firmicutes</italic> 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 <italic>Caryophanaceae</italic>/<italic>Planococcaceae</italic> 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 <italic>Caryophanaceae</italic>/<italic>Planococcaceae</italic> 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 <italic>Caryophanaceae</italic>/<italic>Planococcaceae</italic>, namely <italic>Metalysinibacillus</italic> gen. nov., <italic>Metasolibacillus</italic> gen. nov., and <italic>Metaplanococcus</italic> gen. nov., as well as the transfer of 25 misclassified species from the families <italic>Caryophanaceae</italic>/<italic>Planococcaceae</italic> and <italic>Bacillaceae</italic> into these three genera and in <italic>Planococcus</italic>, <italic>Solibacillus</italic>, <italic>Sporosarcina</italic>, and <italic>Ureibacillus</italic> genera. These amendments establish a coherent taxonomy and evolutionary history for the family <italic>Caryophanaceae</italic>/<italic>Planococcaceae</italic>, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family <italic>Planococcaceae</italic> within the emended family <italic>Caryophanaceae</italic>.</p>