Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacte

@article{Gupta2013MolecularSF,
  title={Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacte},
  author={Radhey S. Gupta and Ricky Lali},
  journal={Antonie van Leeuwenhoek},
  year={2013},
  volume={104},
  pages={349-368}
}
We report here detailed phylogenetic and comparative analyses on 11 sequenced genomes from the phylum Aquificae to identify molecular markers that are specific for the species from this phylum or its different families (viz. Aquificaceae,Hydrogenothermaceae and Desulfurobacteriaceae). In phylogenetic trees based on 16S rRNA gene or concatenated sequences for 32 conserved proteins, species from the three Aquificae families formed distinct clades. These trees also supported a strong relationship… 
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Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) a
TLDR
The results of phylogenetic/compatibility studies along with the species distribution patterns of 22 identified CSIs provide compelling evidence that the current genus Thermotoga is comprised of two evolutionary distinct groups and that it should be divided into two genera.
Erratum to: Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae
TLDR
The results of phylogenetic/compatibility studies along with the species distribution patterns of 22 identified CSIs provide compelling evidence that the current genus Thermotoga is comprised of two evolutionary distinct groups and that it should be divided into two genera.
A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae
TLDR
A comprehensive comparative analysis of 129 sequenced genomes from members of the class Halobacteria is completed in order to identify shared molecular characteristics, in the forms of conserved signature insertions/deletions (CSIs) and Conserved signature proteins (CSPs), which can provide reliable evidence, independent of phylogenetic trees, that the species from the groups in which they are found are specifically related to each other due to common ancestry.
Phylogenomic and Molecular Demarcation of the Core Members of the Polyphyletic Pasteurellaceae Genera Actinobacillus, Haemophilus, and Pasteurella
TLDR
Molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses are utilized to clarify the phylogenetic and taxonomic boundary of the genera Actinobacillus, Haemophilus, and Pasteurella.
Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives
TLDR
A novel molecular signature identified in this work that is uniquely shared by the akinete-forming heterocystous cyanob bacteria provides further evidence that the members of this group are specifically related and they shared a common ancestor exclusive of the other cyanobacteria.
Identification of distinctive molecular traits that are characteristic of the phylum "Deinococcus-Thermus" and distinguish its main constituent groups.
Genomewide comparison and novel ncRNAs of Aquificales
TLDR
The Aquificales, a group of bacteria thriving in extreme environments, are re-analyzed, sharing the feature of a small, compact genome with a reduced number of protein and ncRNA genes, and several classical ncRNAs and riboswitch candidates are presented.
Chapter 8 – Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies
Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)
TLDR
Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss.
Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification.
TLDR
Multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs, which strongly support Darwin's views on evolution and classification.
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