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…Â
30 Citations
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
- BiologyAntonie van Leeuwenhoek
- 2013
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
- BiologyAntonie van Leeuwenhoek
- 2015
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
- BiologyAntonie van Leeuwenhoek
- 2016
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
- BiologyInternational journal of genomics
- 2015
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
- BiologyPhotosynthesis Research
- 2014
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.
- BiologySystematic and applied microbiology
- 2016
Genomewide comparison and novel ncRNAs of Aquificales
- BiologyBMC Genomics
- 2013
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
- Biology
- 2014
Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)
- BiologyProtoplasma
- 2020
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.
- BiologyFEMS microbiology reviews
- 2016
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.
References
SHOWING 1-10 OF 75 REFERENCES
Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov.
- BiologyAntonie van Leeuwenhoek
- 2012
It is suggested that the phylum Chloroflexi “sensu stricto” should be comprised only of the classes Chlor oflexi and Thermomicrobia and the other four classes (viz. Dehalococcoidetes, Anaerolineae, Caldilineae and Ktedonobacteria), which is supported by both phylogenetic means and the identified CSIs.
Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Egger
- BiologyInternational journal of systematic and evolutionary microbiology
- 2013
Detailed phylogenetic and comparative analyses on 22 sequenced genomes from members of the class Coriobacteriia have identified 66 conserved signature inserts or deletions in widely distributed proteins that are specific for a number of different clades of this class at multiple phylogenetic levels.
Phylogenetic Position of Aquificales Based on the Whole Genome Sequences of Six Aquificales Species
- Biology, Environmental ScienceInternational journal of evolutionary biology
- 2012
This work reconstructed the phylogenetic trees of 18 bacteria including six Aquificales species based on the concatenated data of proteins shared by these bacteria, and found that many proteins phylogenetically related to the ε-proteobacteria may be encoded in the genomes of the members of the AquifICALes.
Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales.
- Biology, Environmental ScienceInternational microbiology : the official journal of the Spanish Society for Microbiology
- 2004
The results provide strong and consistent evidence that the Aquificales diverged after the branching of Firmicutes, Actinob bacteria, Thermotoga, Deinococcus-Thermus, green nonsulfur bacteria, Cyanobacteria, Spirochetes, Chlamydiae, and CFBG group, but before the emergence of the Proteobacteria.
Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria
- BiologyMicrobiology and Molecular Reviews
- 2012
Large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades at various taxonomic levels enable the development of a stable and reliable phylogenetic framework for this phylum.
Molecular signatures in protein sequences that are characteristics of the phylum Aquificae.
- BiologyInternational journal of systematic and evolutionary microbiology
- 2006
Six conserved inserts and deletions (indels or signature sequences) in four widely distributed proteins that are distinctive features of species from the phylum Aquificae are described and may prove useful for functional studies aimed at understanding the unique biochemical and physiological characteristics of these species.
Molecular signatures for the phylum Synergistetes and some of its subclades
- BiologyAntonie van Leeuwenhoek
- 2012
Identification of 32 CSIs in widely distributed proteins that provide novel molecular markers that distinguish the species of the phylum Synergistetes from all other bacteria suggest novel targets for evolutionary, genetic and biochemical studies on these bacteria as well as for the identification of additional species belonging to this phylum in different environments.
Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus.
- BiologyInternational journal of systematic and evolutionary microbiology
- 2013
The molecular markers identified in this study provide a reliable means for the reorganization of the currently polyphyletic genus Bacillus into a more evolutionarily consistent set of groups.
Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution
- BiologyFront. Cell. Inf. Microbio.
- 2012
Evidence is provided that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships, as well as novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.
Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria.
- BiologyInternational journal of systematic and evolutionary microbiology
- 2009
75 proteins that were unique to most members of the class Gammaproteobacteria or were restricted to species from some of its main orders are identified, suggesting that species from these orders shared a common ancestor that was separate from other bacteria.