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Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms.

Tamames J, Sánchez PD, Nikel PI, Pedrós-Alió C - Front Microbiol (2016)

Bottom Line: The combination of these three datasets made it possible to describe and quantify the relationships among them.We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations.Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain.

ABSTRACT
Two complementary forces shape microbial genomes: vertical inheritance of genes by phylogenetic descent, and acquisition of new genes related to adaptation to particular habitats and lifestyles. Quantification of the relative importance of each driving force proved difficult. We determined the contribution of each factor, and identified particular genes or biochemical/cellular processes linked to environmental preferences (i.e., propensity of a taxon to live in particular habitats). Three types of data were confronted: (i) complete genomes, which provide gene content of different taxa; (ii) phylogenetic information, via alignment of 16S rRNA sequences, which allowed determination of the distance between taxa, and (iii) distribution of species in environments via 16S rRNA sampling experiments, reflecting environmental preferences of different taxa. The combination of these three datasets made it possible to describe and quantify the relationships among them. We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations. Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing. These genes are likely important for adaptation of bacteria to particular conditions or habitats, such as carbohydrate or glycan metabolism genes being linked to host-associated environments.

No MeSH data available.


Related in: MedlinePlus

Relationships between phylogenetic distance and gene content and environmental correlations. Box-plots have been generated as explained in Figure S3, and show the quantification of the relationships between the three distances. Boxes are generated by discretizing the variable in the x-axis, and show the distribution of the measures in the y-axis corresponding to that discrete values in x. Therefore, the plots explain how the variable in y responds to the changes in x. Permuting the axes changes the discretization to the other variable. The boxes correspond to upper and lower quartiles of the data, and the marks within correspond to the median. Lines outside boxes (whiskers) show the variability outside the boxes, as an indication of the dispersion of the data. The plots shows how gene content similarity responds to: (A) phylogenetic distance, or (B) environmental correlation.
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Figure 5: Relationships between phylogenetic distance and gene content and environmental correlations. Box-plots have been generated as explained in Figure S3, and show the quantification of the relationships between the three distances. Boxes are generated by discretizing the variable in the x-axis, and show the distribution of the measures in the y-axis corresponding to that discrete values in x. Therefore, the plots explain how the variable in y responds to the changes in x. Permuting the axes changes the discretization to the other variable. The boxes correspond to upper and lower quartiles of the data, and the marks within correspond to the median. Lines outside boxes (whiskers) show the variability outside the boxes, as an indication of the dispersion of the data. The plots shows how gene content similarity responds to: (A) phylogenetic distance, or (B) environmental correlation.

Mentions: The relationships among these three measures were examined by looking separately at each side of the cube in Figure 4. The corresponding data are shown as box-plots in Figure 5 and Figures S9, S10 in the Supplementary Material (see Materials and methods and Figure S3 in the Supplementary Material for a detailed explanation of the creation of these box-plots). To aid in interpretation, Figure S7 in the Supplementary Material provides the correspondence between phylogenetic distance and taxonomic ranks.


Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms.

Tamames J, Sánchez PD, Nikel PI, Pedrós-Alió C - Front Microbiol (2016)

Relationships between phylogenetic distance and gene content and environmental correlations. Box-plots have been generated as explained in Figure S3, and show the quantification of the relationships between the three distances. Boxes are generated by discretizing the variable in the x-axis, and show the distribution of the measures in the y-axis corresponding to that discrete values in x. Therefore, the plots explain how the variable in y responds to the changes in x. Permuting the axes changes the discretization to the other variable. The boxes correspond to upper and lower quartiles of the data, and the marks within correspond to the median. Lines outside boxes (whiskers) show the variability outside the boxes, as an indication of the dispersion of the data. The plots shows how gene content similarity responds to: (A) phylogenetic distance, or (B) environmental correlation.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814473&req=5

Figure 5: Relationships between phylogenetic distance and gene content and environmental correlations. Box-plots have been generated as explained in Figure S3, and show the quantification of the relationships between the three distances. Boxes are generated by discretizing the variable in the x-axis, and show the distribution of the measures in the y-axis corresponding to that discrete values in x. Therefore, the plots explain how the variable in y responds to the changes in x. Permuting the axes changes the discretization to the other variable. The boxes correspond to upper and lower quartiles of the data, and the marks within correspond to the median. Lines outside boxes (whiskers) show the variability outside the boxes, as an indication of the dispersion of the data. The plots shows how gene content similarity responds to: (A) phylogenetic distance, or (B) environmental correlation.
Mentions: The relationships among these three measures were examined by looking separately at each side of the cube in Figure 4. The corresponding data are shown as box-plots in Figure 5 and Figures S9, S10 in the Supplementary Material (see Materials and methods and Figure S3 in the Supplementary Material for a detailed explanation of the creation of these box-plots). To aid in interpretation, Figure S7 in the Supplementary Material provides the correspondence between phylogenetic distance and taxonomic ranks.

Bottom Line: The combination of these three datasets made it possible to describe and quantify the relationships among them.We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations.Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain.

ABSTRACT
Two complementary forces shape microbial genomes: vertical inheritance of genes by phylogenetic descent, and acquisition of new genes related to adaptation to particular habitats and lifestyles. Quantification of the relative importance of each driving force proved difficult. We determined the contribution of each factor, and identified particular genes or biochemical/cellular processes linked to environmental preferences (i.e., propensity of a taxon to live in particular habitats). Three types of data were confronted: (i) complete genomes, which provide gene content of different taxa; (ii) phylogenetic information, via alignment of 16S rRNA sequences, which allowed determination of the distance between taxa, and (iii) distribution of species in environments via 16S rRNA sampling experiments, reflecting environmental preferences of different taxa. The combination of these three datasets made it possible to describe and quantify the relationships among them. We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations. Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing. These genes are likely important for adaptation of bacteria to particular conditions or habitats, such as carbohydrate or glycan metabolism genes being linked to host-associated environments.

No MeSH data available.


Related in: MedlinePlus