Visualization of ribosomal RNA operon copy number distribution
<p>Abstract</p> <p>Background</p> <p>Results of microbial ecology studies using 16S rRNA sequence information can be deceiving due to differences in rRNA operon copy number and genome size of the detected organisms. It therefore will be useful for investigators to have...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-09-01
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| Series: | BMC Microbiology |
| Online Access: | http://www.biomedcentral.com/1471-2180/9/208 |
| _version_ | 1811329387609456640 |
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| author | DasGupta Indrani Wu Martin Rastogi Rajat Fox George E |
| author_facet | DasGupta Indrani Wu Martin Rastogi Rajat Fox George E |
| author_sort | DasGupta Indrani |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Results of microbial ecology studies using 16S rRNA sequence information can be deceiving due to differences in rRNA operon copy number and genome size of the detected organisms. It therefore will be useful for investigators to have a better understanding of how these two parameters differ in various organism types. In this study, the number of ribosomal operons and genome size were separately mapped onto a Bacterial phylogenetic tree.</p> <p>Results</p> <p>A representative Bacterial tree was constructed using 31 marker genes found in 578 bacterial genome sequences. Organism names are displayed on the trees using graduations of color such that similar colors indicate similar numbers of operons or genome size. The resulting images provide an intuitive understanding of how copy number and genome size vary in different Bacterial phyla.</p> <p>Conclusion</p> <p>Once the phylogenetic position of a novel organism is known the number of rRNA operons, and to a lesser extent the genome size, can be estimated by examination of the colored maps. Further detail can then be obtained for members of relevant taxa from the rrnDB database.</p> |
| first_indexed | 2024-04-13T15:42:59Z |
| format | Article |
| id | doaj.art-580dc0be091c4a8ab6aa06334079ef8f |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-04-13T15:42:59Z |
| publishDate | 2009-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-580dc0be091c4a8ab6aa06334079ef8f2022-12-22T02:41:04ZengBMCBMC Microbiology1471-21802009-09-019120810.1186/1471-2180-9-208Visualization of ribosomal RNA operon copy number distributionDasGupta IndraniWu MartinRastogi RajatFox George E<p>Abstract</p> <p>Background</p> <p>Results of microbial ecology studies using 16S rRNA sequence information can be deceiving due to differences in rRNA operon copy number and genome size of the detected organisms. It therefore will be useful for investigators to have a better understanding of how these two parameters differ in various organism types. In this study, the number of ribosomal operons and genome size were separately mapped onto a Bacterial phylogenetic tree.</p> <p>Results</p> <p>A representative Bacterial tree was constructed using 31 marker genes found in 578 bacterial genome sequences. Organism names are displayed on the trees using graduations of color such that similar colors indicate similar numbers of operons or genome size. The resulting images provide an intuitive understanding of how copy number and genome size vary in different Bacterial phyla.</p> <p>Conclusion</p> <p>Once the phylogenetic position of a novel organism is known the number of rRNA operons, and to a lesser extent the genome size, can be estimated by examination of the colored maps. Further detail can then be obtained for members of relevant taxa from the rrnDB database.</p>http://www.biomedcentral.com/1471-2180/9/208 |
| spellingShingle | DasGupta Indrani Wu Martin Rastogi Rajat Fox George E Visualization of ribosomal RNA operon copy number distribution BMC Microbiology |
| title | Visualization of ribosomal RNA operon copy number distribution |
| title_full | Visualization of ribosomal RNA operon copy number distribution |
| title_fullStr | Visualization of ribosomal RNA operon copy number distribution |
| title_full_unstemmed | Visualization of ribosomal RNA operon copy number distribution |
| title_short | Visualization of ribosomal RNA operon copy number distribution |
| title_sort | visualization of ribosomal rna operon copy number distribution |
| url | http://www.biomedcentral.com/1471-2180/9/208 |
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