2004
DOI: 10.1111/j.1462-2920.2004.00617.x
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Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins

Abstract: Molecular characterizations of bacteria often employ ribosomal DNA (rDNA) to establish the identity and relationships among organisms, but the use of rRNA sequences can be problematic as the result of alignment ambiguities caused by indels, the lack of informative characters, and varying functional constraints over the molecule. Although protein-coding regions have been used as an alternative to rRNA, there is neither consensus among the genes examined nor ways to rapidly obtain sequence information for such g… Show more

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Cited by 220 publications
(163 citation statements)
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“…We needed a more precise measure of the genetic relatedness between any two strains. The main limitation to a universal measure for all prokaryotic taxa is the lack of genes that are widely distributed in all taxa, e.g., recent estimates suggest that there are Ͻ100 such genes (23,24). Even these widely distributed genes, however, frequently show conflicting values of genetic relatedness because of their varied evolutionary histories (mutation rate and selection pressures) and the as-yet-unclear and not quantifiable effect of horizontal gene transfer (HGT).…”
Section: Cds Functional Annotation and Intergenicmentioning
confidence: 99%
“…We needed a more precise measure of the genetic relatedness between any two strains. The main limitation to a universal measure for all prokaryotic taxa is the lack of genes that are widely distributed in all taxa, e.g., recent estimates suggest that there are Ͻ100 such genes (23,24). Even these widely distributed genes, however, frequently show conflicting values of genetic relatedness because of their varied evolutionary histories (mutation rate and selection pressures) and the as-yet-unclear and not quantifiable effect of horizontal gene transfer (HGT).…”
Section: Cds Functional Annotation and Intergenicmentioning
confidence: 99%
“…The appeal is that any uncharacterized organism, whether cultured or not, can be readily placed onto the tree of life by its 16S rRNA sequence (Harris et al 2004); efforts are underway to make possible a universal tree based on the protein sequences (Zeigler 2003;Santos & Ochman 2004). Moreover, Stackebrandt & Goebbel (1994) have determined an empirical relationship between levels of 16S sequence divergence and annealing by DNA-DNA hybridization.…”
Section: The 'Species' Of Bacterial Systematicsmentioning
confidence: 99%
“…However, 16S rRNA gene sequence data do not allow the identification of closely related species. The use of housekeeping genes is emerging as an alternative to overcome these problems (Santos & Ochman, 2004;Stackebrandt et al, 2002). Recent in silico studies based on complete genomes have provided the basis for establishing sets of housekeeping genes that can accurately predict genome relatedness and improve the accuracy of species identification.…”
Section: Introductionmentioning
confidence: 99%