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Journal article
Prokaryotic Nucleotide Composition Is Shaped by Both Phylogeny and the Environment
Genome biology and evolution, v 7(5), pp 1380-1389
01 May 2015
PMID: 25861819
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences-which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.
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Details
- Title
- Prokaryotic Nucleotide Composition Is Shaped by Both Phylogeny and the Environment
- Creators
- Erin R. Reichenberger - Drexel UniversityGail Rosen - Drexel UniversityUri Hershberg - Drexel UniversityRuth Hershberg - Rappaport Faculty of MedicineDrexel Univ., Philadelphia, PA (United States)
- Publication Details
- Genome biology and evolution, v 7(5), pp 1380-1389
- Publisher
- Oxford Univ Press
- Number of pages
- 10
- Grant note
- Ford Foundation fellowship P01AI106697 / National Institute of Allergy and Infectious Diseases of the National Institute of Health DE-SC0004335 / Department of Energy (DOE) Office of Science (BER) award; United States Department of Energy (DOE) 321780 / ERC FP7 CIG grant P01AI106697 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) 1120622 / NSF; National Science Foundation (NSF) Louis and Bessie Stein Foundation Robert J. Shillman Career Advancement Chair 0845827 / National Science Foundation (NSF) CAREER award; National Science Foundation (NSF); NSF - Office of the Director (OD) 2013463 / BSF grant by a Yigal Allon Fellowship - Israeli Council for Higher Education
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Electrical and Computer Engineering; School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000356228800017
- Scopus ID
- 2-s2.0-84940873445
- Other Identifier
- 991019168973604721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Evolutionary Biology
- Genetics & Heredity