Exploration of phylogenetic data using a global sequence analysis method

Chapus, Charles; Dufraigne, Christine; Edwards, Scott V.; Giron, Alain; Fertil, Bernard; Deschavanne, Patrick

doi:10.1186/1471-2148-5-63

Cited by 41 publications

(22 citation statements)

References 63 publications

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“…The genomic signature tree was built using GOHTAM by neighbor joining the pairwise comparison matrix of the 4-nucleotide word frequencies of all-versus-all taxa with an Euclidean distance [ 55 ]. The resulting distances and scale are subsequently converted into arbitrary units.…”

Section: Methodsmentioning

confidence: 99%

Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation

et al. 2017

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The unique ability of the tuberculosis (TB) bacillus, Mycobacterium tuberculosis, to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB. We and others previously reported that the M. tuberculosis ancestor underwent massive episodes of horizontal gene transfer (HGT), mostly from environmental species. Here, we sought to explore whether such ancient HGT played a part in M. tuberculosis evolution towards pathogenicity. We were interested by a HGT-acquired M. tuberculosis-specific gene set, namely moaA1-D1, which is involved in the biosynthesis of the molybdenum cofactor. Horizontal acquisition of this gene set was striking because homologues of these moa genes are present all across the Mycobacterium genus, including in M. tuberculosis. Here, we discovered that, unlike their paralogues, the moaA1-D1 genes are strongly induced under hypoxia. In vitro, a M. tuberculosis moaA1-D1-null mutant has an impaired ability to respire nitrate, to enter dormancy and to survive in oxygen-limiting conditions. Conversely, heterologous expression of moaA1-D1 in the phylogenetically closest non-TB mycobacterium, Mycobacterium kansasii, which lacks these genes, improves its capacity to respire nitrate and grants it with a marked ability to survive oxygen depletion. In vivo, the M. tuberculosis moaA1-D1-null mutant shows impaired survival in hypoxic granulomas in C3HeB/FeJ mice, but not in normoxic lesions in C57BL/6 animals. Collectively, our results identify a novel pathway required for M. tuberculosis resistance to host-imposed stress, namely hypoxia, and provide evidence that ancient HGT bolstered M. tuberculosis evolution from an environmental species towards a pervasive human-adapted pathogen.

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Section: Methodsmentioning

confidence: 99%

Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation

et al. 2017

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“…In [ 16 ], 20 mammalian complete mtDNA sequences were analyzed using the “similarity metric”, for k =7. In [ 50 ] a multigene dataset of 33 genes for 9 bacteria and one archaea species, as well as the whole genomes of a set of 16 γ -proteobacteria were analyzed, using values of k between 1 and 10, and Euclidean and χ 2 distances. In [ 11 ] a collection of 26 complete mitochondrial genomes was analyzed, using the Euclidean distance and an “image distance”, with a value of k =10.…”

Section: Introductionmentioning

confidence: 99%

An investigation into inter- and intragenomic variations of graphic genomic signatures

et al. 2015

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BackgroundMotivated by the general need to identify and classify species based on molecular evidence, genome comparisons have been proposed that are based on measuring mostly Euclidean distances between Chaos Game Representation (CGR) patterns of genomic DNA sequences.ResultsWe provide, on an extensive dataset and using several different distances, confirmation of the hypothesis that CGR patterns are preserved along a genomic DNA sequence, and are different for DNA sequences originating from genomes of different species. This finding lends support to the theory that CGRs of genomic sequences can act as graphic genomic signatures. In particular, we compare the CGR patterns of over five hundred different 150,000 bp genomic sequences spanning one complete chromosome from each of six organisms, representing all kingdoms of life: H. sapiens (Animalia; chromosome 21), S. cerevisiae (Fungi; chromosome 4), A. thaliana (Plantae; chromosome 1), P. falciparum (Protista; chromosome 14), E. coli (Bacteria - full genome), and P. furiosus (Archaea - full genome). To maximize the diversity within each species, we also analyze the interrelationships within a set of over five hundred 150,000 bp genomic sequences sampled from the entire aforementioned genomes. Lastly, we provide some preliminary evidence of this method’s ability to classify genomic DNA sequences at lower taxonomic levels by comparing sequences sampled from the entire genome of H. sapiens (class Mammalia, order Primates) and of M. musculus (class Mammalia, order Rodentia), for a total length of approximately 174 million basepairs analyzed. We compute pairwise distances between CGRs of these genomic sequences using six different distances, and construct Molecular Distance Maps, which visualize all sequences as points in a two-dimensional or three-dimensional space, to simultaneously display their interrelationships.ConclusionOur analysis confirms, for this dataset, that CGR patterns of DNA sequences from the same genome are in general quantitatively similar, while being different for DNA sequences from genomes of different species. Our assessment of the performance of the six distances analyzed uses three different quality measures and suggests that several distances outperform the Euclidean distance, which has so far been almost exclusively used for such studies.

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“…Alignment-free methods are based on sets of short oligonucleotides taken from the genome to infer phylogenies and often produce similar results as traditional methods (Chapus et al, 2005). The basic principle behind alignment-free phylogenetic tree reconstruction techniques is that genomic subsequences exhibit similar characteristics as the whole genome (Deschavanne et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

CAM: an alignment-free method to recover phylogenies using codon aversion motifs

Miller

McKinnon

Whiting

et al. 2019

PeerJ

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Background Common phylogenomic approaches for recovering phylogenies are often time-consuming and require annotations for orthologous gene relationships that are not always available. In contrast, alignment-free phylogenomic approaches typically use structure and oligomer frequencies to calculate pairwise distances between species. We have developed an approach to quickly calculate distances between species based on codon aversion. Methods Utilizing a novel alignment-free character state, we present CAM, an alignment-free approach to recover phylogenies by comparing differences in codon aversion motifs (i.e., the set of unused codons within each gene) across all genes within a species. Synonymous codon usage is non-random and differs between organisms, between genes, and even within a single gene, and many genes do not use all possible codons. We report a comprehensive analysis of codon aversion within 229,742,339 genes from 23,428 species across all kingdoms of life, and we provide an alignment-free framework for its use in a phylogenetic construct. For each species, we first construct a set of codon aversion motifs spanning all genes within that species. We define the pairwise distance between two species, A and B, as one minus the number of shared codon aversion motifs divided by the total codon aversion motifs of the species, A or B, containing the fewest motifs. This approach allows us to calculate pairwise distances even when substantial differences in the number of genes or a high rate of divergence between species exists. Finally, we use neighbor-joining to recover phylogenies. Results Using the Open Tree of Life and NCBI Taxonomy Database as expected phylogenies, our approach compares well, recovering phylogenies that largely match expected trees and are comparable to trees recovered using maximum likelihood and other alignment-free approaches. Our technique is much faster than maximum likelihood and similar in accuracy to other alignment-free approaches. Therefore, we propose that codon aversion be considered a phylogenetically conserved character that may be used in future phylogenomic studies. Availability CAM, documentation, and test files are freely available on GitHub at https://github.com/ridgelab/cam.

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Exploration of phylogenetic data using a global sequence analysis method

Abstract: Background: Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.

Cited by 41 publications

References 63 publications

Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation

Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation

An investigation into inter- and intragenomic variations of graphic genomic signatures

CAM: an alignment-free method to recover phylogenies using codon aversion motifs

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