Microbial Phylogeny and Evolution Based on Protein Sequences (The Change from Targeted Genes to Proteins)

Gupta, Radhey S.

doi:10.1002/9780470665497.ch2

Cited by 3 publications

(1 citation statement)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The markers that are ideally suited for evolutionary and systematic studies are those that are generally not affected by factors such as multiple changes at a given site, long-branch attraction effects, differences in evolutionary rates, and lateral gene transfers, etc., which confound the inferences from phylogenetic trees (10,81,82,119,126,130,206). Two types of molecular markers that generally satisfy these characteristics have been identified recently for a number of bacterial phyla, and they are proving to be of great value in our understanding of bacterial phylogeny and systematics (124,126,127,130,132,133,179).…”

Section: Usefulness Of Conserved Signature Indels and Signature Protementioning

confidence: 99%

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

Gao

Gupta

2012

Microbiol Mol Biol Rev

Self Cite

243

237

View full text Add to dashboard Cite

SUMMARY The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe 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 ( viz ., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia ) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria . The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria -specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria .

show abstract

Section: Usefulness Of Conserved Signature Indels and Signature Protementioning

confidence: 99%

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

Gao

Gupta

2012

Microbiol Mol Biol Rev

Self Cite

243

237

View full text Add to dashboard Cite

show abstract

A Paradigm Shift from Research to Front‐Line Microbial Diagnostics in MALDI‐TOF and LC‐MS/MS

Shah

Gharbia

2017

MALDI‐TOF and Tandem MS for Clinical Microbiology

View full text Add to dashboard Cite

Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification

Gupta¹

2016

FEMS Microbiology Reviews

131

View full text Add to dashboard Cite

Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, 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. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa.

show abstract

Microbial Phylogeny and Evolution Based on Protein Sequences (The Change from Targeted Genes to Proteins)

Cited by 3 publications

References 69 publications

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

A Paradigm Shift from Research to Front‐Line Microbial Diagnostics in MALDI‐TOF and LC‐MS/MS

Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification

Contact Info

Product

Resources

About