A strategy for sequence phylogeny research

Sankoff, David; Cedergren, Robert; McKay, Wendy

doi:10.1093/nar/10.1.421

Cited by 48 publications

(12 citation statements)

References 12 publications

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“…strain BC3 (14), M. capricolum (21), and M. mycoides capri (14) have been reported previously. The residue U has been inserted into position 8 4 and 121. Both Anaeroplasma species had identical sequences, so only one is shown here.…”

Section: Resultsmentioning

confidence: 99%

Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data.

Rogers¹,

Simmons²,

Walker³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

162

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The 5S rRNA sequences of eubacteria and mycoplasmas have been analyzed and a phylogenetic tree constructed. We determined the sequences of 5S rRNA from CMstridium innocuum, Acholeplasma laidlawii, Acholeplasma modicum, Anaeroplasma bactoclasticum, Anaeroplasma abactoclasticum, Ureaplasma urealyticum, Mycoplasma mycoides mycoides, Mycoplasma pneumoniae, and Mycoplasma gallisepticum. Analysis of these and published sequences shows that mycoplasmas form a coherent phylogenetic group that, with C. innocuum, arose as a branch of the low G+C Gram-positive tree, near the lactobacilli and streptococci. The initial event in mycoplasma phylogeny was formation of the Acholeplasma branch; hence, loss of cell wall probably occurred at the time of genome reduction to lO000 MDa. A subsequent branch produced the Spiroplasma. This branch appears to have been the origin of sterol-requiring mycoplasmas. During development of the Spiroplasma branch there were several independent genome reductions, each to -500 MDa, resulting in Mycoplasma and Ureaplasma species. Mycoplasmas, particularly species with the smallest genomes, have high mutation rates, suggesting that they are in a state of rapid evolution.The wall-less prokaryotes are grouped in the class Mollicutes and are referred to as mycoplasmas (1). Mycoplasma genera (Table 1) are diverse in terms of their biochemistry, ecological niches, and genome structure. In addition, some of these organisms are significant animal, plant, and insect pathogens. Two aspects of mycoplasma biology are of particular interest. First, some mycoplasmas (i.e., Spiroplasma, Mycoplasma, Ureaplasma, and some Anaeroplasma species) are the only prokaryotes known to require cholesterol for growth; and, second, mycoplasmas have the smallest amounts of genetic information of any free-living organisms. Mycoplasma DNAs contain a low percentage of G+C.Mycoplasma genomes fall into two size classes. Acholeplasma, Spiroplasma, and Thermoplasma genomes are "1000 MDa, a size that is rare but not unknown among eubacteria (reviewed in ref.2). Mycoplasma and Ureaplasma genomes are "500 MDa, the smallest reported cellular genomes. This is only slightly larger than the theoretical minimal amount of genetic information for a cellular system (4), indicating that the complexity of mycoplasma cells must be constrained by their limited genome content.The origin and phylogenetic relationships of mycoplasmas have been of interest because these cells are the result of natural selection operating within the constraint of limited genome complexity. In the past decade, a number of studies indicated that particular biochemical properties of some Mycoplasma and Acholeplasma species are closer to those of Gram-positive than to Gram-negative eubacteria (reviewed in refs. 2 and 3). A more complete view of mycoplasma evolution came from a recent comparative analysis of 16S rRNA oligonucleotide catalogs of Acholeplasma laidlawii, Spiroplasma citri, Mycoplasma capricolum, Mycoplasma gallisepticum, and Thermoplasma acidophilum with ...

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Section: Resultsmentioning

confidence: 99%

Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data.

Rogers¹,

Simmons²,

Walker³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

162

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“…Despite interest in tRNA phylogeny as a source of information about the evolution of the genetic code (Eigen and Winkler-Oswatitsch 1981a,b;Fitch and Upper 1987;Eigen et al 1989;Di Giulio 1994, 1995, 1999, 2006, and, although tRNAs were among the first nucleic acid sequences to be used for phylogenetic reconstruction (Cedergren et al 1980;Sankoff et al 1982), the phylogenetic trees obtained from tRNAs are often radically different from the trees relating the species. tRNAs are now considered especially poor candidates for phylogenetic studies for several reasons.…”

Section: Introductionmentioning

confidence: 99%

Stable tRNA-based phylogenies using only 76 nucleotides

Widmann

Harris²,

Lozupone³

et al. 2010

RNA

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tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity. Here we use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life based on the phylogenetic relationships among their complete tRNA pools. We find that the overall pattern of similarities and differences in the tRNA pools recaptures universal phylogeny to a remarkable extent, and that the resulting tree is similar to the distribution of bootstrapped rRNA trees from the same genomes. In contrast, the trees derived from tRNAs of identical specificity or of individual isoacceptors generally produced trees of lower quality. However, some tRNA isoacceptors were very good predictors of the overall pattern of organismal evolution. These results show that UniFrac can extract meaningful biological patterns from even phylogenies with high level of statistical inaccuracy and horizontal gene transfer, and that, overall, the pattern of tRNA evolution tracks universal phylogeny and provides a background against which we can test hypotheses about the evolution of individual isoacceptors.

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“…The interrelationships in a set of amino acid sequences (the primary structures of proteins) are commonly represented as a tree (Fitch and Margoliash 1967;Moore et al 1973;Sankoff et al 1982;Penny and Hendy 1986). In such a tree the distance (dissimilarity) between any pair of sequences is approximately the length of the unique path connecting the corresponding nodes (additivity).…”

Section: Introductionmentioning

confidence: 99%

Phylogeny reconstruction for protein sequences based on amino acid properties

Schmidt

1995

J Mol Evol

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This paper presents an essentially new method used to construct phylogenetic trees from related amino acid sequences. The method is based on a new distance measure which describes sequence relationships by means of typical steric and physicochemical properties of the amino acids and is advantageous in some essential points. The method was applied to different sets of protein sequences and the results were compared with other well-established methods.

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A strategy for sequence phylogeny research

Cited by 48 publications

References 12 publications

Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data.

Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data.

Stable tRNA-based phylogenies using only 76 nucleotides

Phylogeny reconstruction for protein sequences based on amino acid properties

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