Prokaryotic genomes: the emerging paradigm of genome-based microbiology
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Cited by (123)
Gifts hidden in shadowy genome islands
2023, CellEvolution of Microbial Genomics: Conceptual Shifts over a Quarter Century
2021, Trends in MicrobiologyCitation Excerpt :This conceptual shift was triggered by the observations, made shortly after the first several complete genomes of bacteria and archaea were sequenced, that phylogenies of different conserved genes had different topologies. The differences were found to be so extensive that they could not be explained away by methodological artifacts, leading to the conclusion that extensive HGT was a key factor in the evolution of prokaryotes [5,70–73]. Hence the idea of giving up the concept of the Tree of Life (ToL) for a net of life, devoid of any vertical component, gained much ground, leading to vivid debates on the extent of 'horizontal genomics' [74–77].
Genome profiling (GP) as an effective tool for monitoring culture collections: A case study with Trichosporon
2012, Journal of Microbiological MethodsCitation Excerpt :Although the sequencing itself is determinate and reliable, the amount of information provided by a single gene sequencing is limited and often insufficient. Thus, it is less favorable in cost-performance and not infallible in classifying species (Fitz-Gibbon and House, 1999; Koonin and Galperin, 1997; Snel et al., 1999). In the case of fungi, the D1/D2 domain of 26S rDNA and ITS (internal transcribed spacer) sequences have been used frequently for identification of species.
Approaches to the study of the systematics of anaerobic, Gram-negative, non-sporeforming rods: Current status and perspectives
2009, AnaerobeCitation Excerpt :The availability of large number of genome sequences from different bacteria provides an unprecedented opportunity for discovering novel molecular properties, which are unique to particular taxonomic groups of bacteria, and that can possibly bridge the gap between phylogenetics and genotypic–phenotypic characteristics. Comparative genomic analyses are providing valuable information regarding many aspects including sets of genes that are present or absent in given groups of species, arrangement of genes in the genomes, genes that have been laterally acquired, conserved inserts and deletions (i.e. indels) and also whole proteins that are specific for a given group of species [87–89]. Of these, the last two characteristics, i.e. conserved indels and whole proteins that are restricted to particular groups, have proven very useful for taxonomic and evolutionary studies [85,90–92].
Whole-genome prokaryotic clustering based on gene lengths
2009, Discrete Applied MathematicsCitation Excerpt :For instance, saturation is a problem due to the length of the ssu-rRNA and functional restrictions limiting the number of possible mutations of this highly conserved RNA-coding gene. Species phylogenies derived from comparisons of single genes are rarely consistent with each other, particularly due to horizontal gene transfer [8,9,30,7]. Another well known problem associated with the traditional approach, is that the evolutionary history of any single gene may differ from the evolutionary history of the whole organism.
GUNC: detection of chimerism and contamination in prokaryotic genomes
2021, Genome Biology