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Journal article
Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
Microbiome, v 4(1), pp 18-18
03 May 2016
PMID: 27138046
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Background: The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels.
Results: In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that the percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage.
Conclusions: Our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.
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Details
- Title
- Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
- Creators
- Yemin Lan - Drexel UniversityGail Rosen - Drexel UniversityRuth Hershberg - Rappaport Faculty of MedicineDrexel Univ., Philadelphia, PA (United States)
- Publication Details
- Microbiome, v 4(1), pp 18-18
- Publisher
- Springer Nature
- Number of pages
- 13
- Grant note
- 2013463 / BSF; US-Israel Binational Science Foundation Louis and Bessie Stein Family Fellowship DE-SC0004335 / Department of Energy (DOE) Office of Science (BER); United States Department of Energy (DOE) 1120622 / NSF; National Science Foundation (NSF) Robert J. Shillman Career Advancement Chair 0845827 / National Science Foundation (NSF) CAREER; National Science Foundation (NSF); NSF - Office of the Director (OD) Israeli Council for Higher Education 321780 / ERC; European Research Council (ERC); European Commission
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Electrical and Computer Engineering
- Web of Science ID
- WOS:000375658000001
- Scopus ID
- 2-s2.0-84995814400
- Other Identifier
- 991019168425504721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Microbiology