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rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development.

Stoddard SF, Smith BJ, Hein R, Roller BR, Schmidt TM - Nucleic Acids Res. (2014)

Bottom Line: Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of microbial communities. rRNA genes are often co-located as part of an rrn operon, and multiple copies of this operon are present in genomes across the microbial tree of life. rrn copy number variability provides valuable insight into microbial life history, but introduces systematic bias when measuring community composition in molecular surveys.Here we present an update to the ribosomal RNA operon copy number database (rrnDB), a publicly available, curated resource for copy number information for bacteria and archaea.The enhanced rrnDB will contribute to the analysis of molecular surveys and to research linking genomic characteristics to life history.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.

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Histogram showing 16S copy number variability in 301 species aggregates of the rrnDB records. Only species that are represented by at least two records are counted in this display. Fully 77% of the species show zero variance in 16S gene copy number count among the comprising records. Sixteen percent of the species vary by only one copy, and only 3% of species show a copy number spread of three or more.
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Figure 3: Histogram showing 16S copy number variability in 301 species aggregates of the rrnDB records. Only species that are represented by at least two records are counted in this display. Fully 77% of the species show zero variance in 16S gene copy number count among the comprising records. Sixteen percent of the species vary by only one copy, and only 3% of species show a copy number spread of three or more.

Mentions: A final QC test looks for genomes having 16S copy number counts that are outside of the usual range displayed by other genomes of its species. Any species group that shows a difference of three or more between the lowest and highest 16S copy number, is manually examined for genomes that are candidates for having annotation errors affecting 16S gene counts. We have used the database to assess 16S copy-number variability in single-species aggregates of records (Figure 3). For 301 species that are represented by at least two records, 77% are invariant within the species for 16S copy number. An additional 16% of species vary by only one 16S copy. Only 3% of species vary by more than two 16S copies and the maximum variability was five (one species represented by two genomes). Seven genomes have been held back by these criteria.


rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development.

Stoddard SF, Smith BJ, Hein R, Roller BR, Schmidt TM - Nucleic Acids Res. (2014)

Histogram showing 16S copy number variability in 301 species aggregates of the rrnDB records. Only species that are represented by at least two records are counted in this display. Fully 77% of the species show zero variance in 16S gene copy number count among the comprising records. Sixteen percent of the species vary by only one copy, and only 3% of species show a copy number spread of three or more.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383981&req=5

Figure 3: Histogram showing 16S copy number variability in 301 species aggregates of the rrnDB records. Only species that are represented by at least two records are counted in this display. Fully 77% of the species show zero variance in 16S gene copy number count among the comprising records. Sixteen percent of the species vary by only one copy, and only 3% of species show a copy number spread of three or more.
Mentions: A final QC test looks for genomes having 16S copy number counts that are outside of the usual range displayed by other genomes of its species. Any species group that shows a difference of three or more between the lowest and highest 16S copy number, is manually examined for genomes that are candidates for having annotation errors affecting 16S gene counts. We have used the database to assess 16S copy-number variability in single-species aggregates of records (Figure 3). For 301 species that are represented by at least two records, 77% are invariant within the species for 16S copy number. An additional 16% of species vary by only one 16S copy. Only 3% of species vary by more than two 16S copies and the maximum variability was five (one species represented by two genomes). Seven genomes have been held back by these criteria.

Bottom Line: Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of microbial communities. rRNA genes are often co-located as part of an rrn operon, and multiple copies of this operon are present in genomes across the microbial tree of life. rrn copy number variability provides valuable insight into microbial life history, but introduces systematic bias when measuring community composition in molecular surveys.Here we present an update to the ribosomal RNA operon copy number database (rrnDB), a publicly available, curated resource for copy number information for bacteria and archaea.The enhanced rrnDB will contribute to the analysis of molecular surveys and to research linking genomic characteristics to life history.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.

Show MeSH