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Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera.

Trost B, Haakensen M, Pittet V, Ziola B, Kusalik A - BMC Microbiol. (2010)

Bottom Line: The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics.We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this relationship varied substantially depending on the genus, perhaps reflecting different rates of genome evolution and/or horizontal gene transfer.The results described in this study aid our understanding of protein content relationships in different bacterial groups, allowing us to make further inferences regarding genome-environment relationships, genome evolution, and the soundness of existing taxonomic classifications.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, University of Saskatchewan, 176 Thorvaldson Building, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada. brett.trost@usask.ca

ABSTRACT

Background: The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacteria, there has yet to be a study that provides a general characterization of protein content relationships in a broad range of bacteria.

Results: A variation on reciprocal BLAST hits was used to infer relationships among proteins in several groups of bacteria, and data regarding protein conservation and uniqueness in different bacterial genera are reported in terms of "core proteomes", "unique proteomes", and "singlets". We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this relationship varied substantially depending on the genus, perhaps reflecting different rates of genome evolution and/or horizontal gene transfer. Finally, core proteomes and unique proteomes were used to study the proteomic cohesiveness of several bacterial species, revealing that some bacterial species had little cohesiveness in their protein content, with some having fewer proteins unique to that species than randomly-chosen sets of isolates from the same genus.

Conclusions: The results described in this study aid our understanding of protein content relationships in different bacterial groups, allowing us to make further inferences regarding genome-environment relationships, genome evolution, and the soundness of existing taxonomic classifications.

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Phylogenetic relationships among the organisms used in this study. Three phylogenetic trees were constructed, each of which used a different distance metric. Panel (A) depicts the tree constructed using the 16S rRNA gene similarity between two isolates, while panels (B) and (C) depict trees based on shared proteins and average unique proteins, respectively. Due to space constraints, collapsed trees are shown; the full trees are available as additional files 2, 3, and 4. The length of the base of each triangle represents the number of species within the genus, while the height indicates the amount of intra-genus divergence.
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Figure 3: Phylogenetic relationships among the organisms used in this study. Three phylogenetic trees were constructed, each of which used a different distance metric. Panel (A) depicts the tree constructed using the 16S rRNA gene similarity between two isolates, while panels (B) and (C) depict trees based on shared proteins and average unique proteins, respectively. Due to space constraints, collapsed trees are shown; the full trees are available as additional files 2, 3, and 4. The length of the base of each triangle represents the number of species within the genus, while the height indicates the amount of intra-genus divergence.

Mentions: As described in the Methods section, we also created three phylogenetic trees, with the first based on 16S rRNA gene similarity, the second based on the number of shared proteins between two isolates, and the third based on the average unique proteins between two isolates. Collapsed versions of these trees are given in Figures 3A, 3B, and 3C, respectively, while trees showing all individual isolates are available as additional files 2, 3 and 4.


Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera.

Trost B, Haakensen M, Pittet V, Ziola B, Kusalik A - BMC Microbiol. (2010)

Phylogenetic relationships among the organisms used in this study. Three phylogenetic trees were constructed, each of which used a different distance metric. Panel (A) depicts the tree constructed using the 16S rRNA gene similarity between two isolates, while panels (B) and (C) depict trees based on shared proteins and average unique proteins, respectively. Due to space constraints, collapsed trees are shown; the full trees are available as additional files 2, 3, and 4. The length of the base of each triangle represents the number of species within the genus, while the height indicates the amount of intra-genus divergence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3020658&req=5

Figure 3: Phylogenetic relationships among the organisms used in this study. Three phylogenetic trees were constructed, each of which used a different distance metric. Panel (A) depicts the tree constructed using the 16S rRNA gene similarity between two isolates, while panels (B) and (C) depict trees based on shared proteins and average unique proteins, respectively. Due to space constraints, collapsed trees are shown; the full trees are available as additional files 2, 3, and 4. The length of the base of each triangle represents the number of species within the genus, while the height indicates the amount of intra-genus divergence.
Mentions: As described in the Methods section, we also created three phylogenetic trees, with the first based on 16S rRNA gene similarity, the second based on the number of shared proteins between two isolates, and the third based on the average unique proteins between two isolates. Collapsed versions of these trees are given in Figures 3A, 3B, and 3C, respectively, while trees showing all individual isolates are available as additional files 2, 3 and 4.

Bottom Line: The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics.We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this relationship varied substantially depending on the genus, perhaps reflecting different rates of genome evolution and/or horizontal gene transfer.The results described in this study aid our understanding of protein content relationships in different bacterial groups, allowing us to make further inferences regarding genome-environment relationships, genome evolution, and the soundness of existing taxonomic classifications.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, University of Saskatchewan, 176 Thorvaldson Building, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada. brett.trost@usask.ca

ABSTRACT

Background: The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacteria, there has yet to be a study that provides a general characterization of protein content relationships in a broad range of bacteria.

Results: A variation on reciprocal BLAST hits was used to infer relationships among proteins in several groups of bacteria, and data regarding protein conservation and uniqueness in different bacterial genera are reported in terms of "core proteomes", "unique proteomes", and "singlets". We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this relationship varied substantially depending on the genus, perhaps reflecting different rates of genome evolution and/or horizontal gene transfer. Finally, core proteomes and unique proteomes were used to study the proteomic cohesiveness of several bacterial species, revealing that some bacterial species had little cohesiveness in their protein content, with some having fewer proteins unique to that species than randomly-chosen sets of isolates from the same genus.

Conclusions: The results described in this study aid our understanding of protein content relationships in different bacterial groups, allowing us to make further inferences regarding genome-environment relationships, genome evolution, and the soundness of existing taxonomic classifications.

Show MeSH