U.S. Department of EnergyOffice of Scientific and Technical Information
KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site
Abstract
Genome assemblies were imported into KBase using the Batch Import Assembly from Staging Area (v1.0.57) function. All assemblies were annotated using the Annotated Multiple Microbial Assemblies with RASTtk - v1.073 tool. Annotated genomes were grouped into sets using the Add Genomes to GenomeSet - v1.7.6 function. Individual annotated genomes can be found both below and in the Data menu to the left. Taxonomy was assigned using the Classify Microbes with GTDB-Tk-v1.7.0 tool. The results of this analysis are shown below. Analysis of the Castellaniella pangenome was performed using the Compute Pangenome (v0.0.7) tool. Using the same method, we also computed the ORR-specific and non-ORR Castellaniella pangenomes. All pangenome results (including the presence/absence matrix) can be found below.
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- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA; Oak Ridge National Laboratory
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA; Department of Chemistry, State University of New York College of Environmental Science and Forestry
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- Earth and Environmental Science Area, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA
- Publication Date:
- Research Org.:
- U.S. Department of Energy Systems Biology Knowledgebase
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 2203552
- DOI:
- https://doi.org/10.25982/135835.33/2203552
Citation Formats
Szink, Elizabeth, Goff, Jennifer, Durrence, Konnor, Lui, Lauren, Nielsen, Torben, Kuehl, Jennifer, Hunt, Kristopher, Chandonia, John-Marc, Thorgersen, Michael, Poole, Farris, Stahl, David, Chakraborty, Romy, Arkin, Adam, and Adams, Michael. KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site. United States: N. p., 2023.
Web. doi:10.25982/135835.33/2203552.
Szink, Elizabeth, Goff, Jennifer, Durrence, Konnor, Lui, Lauren, Nielsen, Torben, Kuehl, Jennifer, Hunt, Kristopher, Chandonia, John-Marc, Thorgersen, Michael, Poole, Farris, Stahl, David, Chakraborty, Romy, Arkin, Adam, & Adams, Michael. KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site. United States. doi:https://doi.org/10.25982/135835.33/2203552
Szink, Elizabeth, Goff, Jennifer, Durrence, Konnor, Lui, Lauren, Nielsen, Torben, Kuehl, Jennifer, Hunt, Kristopher, Chandonia, John-Marc, Thorgersen, Michael, Poole, Farris, Stahl, David, Chakraborty, Romy, Arkin, Adam, and Adams, Michael. 2023.
"KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site". United States. doi:https://doi.org/10.25982/135835.33/2203552. https://www.osti.gov/servlets/purl/2203552. Pub date:Thu Oct 26 00:00:00 EDT 2023
@article{osti_2203552,
title = {KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site},
author = {Szink, Elizabeth and Goff, Jennifer and Durrence, Konnor and Lui, Lauren and Nielsen, Torben and Kuehl, Jennifer and Hunt, Kristopher and Chandonia, John-Marc and Thorgersen, Michael and Poole, Farris and Stahl, David and Chakraborty, Romy and Arkin, Adam and Adams, Michael},
abstractNote = {Genome assemblies were imported into KBase using the Batch Import Assembly from Staging Area (v1.0.57) function. All assemblies were annotated using the Annotated Multiple Microbial Assemblies with RASTtk - v1.073 tool. Annotated genomes were grouped into sets using the Add Genomes to GenomeSet - v1.7.6 function. Individual annotated genomes can be found both below and in the Data menu to the left. Taxonomy was assigned using the Classify Microbes with GTDB-Tk-v1.7.0 tool. The results of this analysis are shown below. Analysis of the Castellaniella pangenome was performed using the Compute Pangenome (v0.0.7) tool. Using the same method, we also computed the ORR-specific and non-ORR Castellaniella pangenomes. All pangenome results (including the presence/absence matrix) can be found below.},
doi = {10.25982/135835.33/2203552},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Thu Oct 26 00:00:00 EDT 2023},
month = {Thu Oct 26 00:00:00 EDT 2023}
}
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