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

Abstract

Gupta and PatelClassification of the Family Caryophanaceae 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.

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

“…However, the branching of species in the 16S rRNA tree is not very reliable. Hence, the assignments based on branching in the 16S rRNA tree should be considered tentative and needs to be confirmed using sequence-based criteria used in our present and previous work [7, 28, 30].…”

“…To further confirm the monophyly of these species clades and reliably demarcate them in molecular terms, detailed studies were carried out on protein sequences from Bacillus species to identify novel molecular markers that are distinctive characteristics of these Bacillus species clades. Our earlier work has established that the conserved signature insertions and deletions (CSIs) in genes/proteins, which are uniquely shared by an evolutionarily related group of organisms, provide an important class of molecular markers for evolutionary and taxonomic studies [28, 30, 32–34, 44, 46, 47]. The CSIs that are useful for these studies are of fixed lengths, present at specific positions in particular genes/proteins, and are flanked on both sides by conserved regions to ensure that the sequence alignment in the region is reliable and that the described CSIs are dependable characteristics [7, 30, 44, 47].…”

“…Identification of conserved signature indels (CSIs) in protein sequences, which are specific for different described clades of Bacillus species, was carried out as described in our recent work [28,30,33,44]. All of the described CSIs are present in conserved regions of the proteins and they are flanked by at least four or five conserved amino acid residues in the neighbouring 40-50 amino acids.…”

“…However, before the genus name Bacillus is restricted to the species from these two clades, it is necessary to reclassify the large numbers of unrelated Bacillus species into other genera. Although many Bacillus species have been reclassified into other genera including, but not limited to, Lysinibacillus, Pseudobacillus, Solibacillus, Alicyclobacillus, Alkalicoccus, Aneurinibacillus, Gracilibacillus, Hydrogenibacillus, Sporosarcina, Ureibacillus and Virgibacillus [21][22][23][24][25][26][27][28][29], until 2019 the genus Bacillus still contained >240 species that were unrelated to the Subtilis or the Cereus clades [1,30].…”

“…Based on the results from this study, >100 Bacillus species encompassing these clades were reclassified into six novel genera ( Alkalihalobacillus, Cytobacillus, Metabacillus, Mesobacillus, Neobacillus and Peribacillus ) [30]. In another recent study, several other misclassified Bacillus species were transferred to specific genera within the family Caryophanaceae [28].…”