KBase Narrative - Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed site

Dataset · Thu Oct 26 00:00:00 EDT 2023

DOI:https://doi.org/10.25982/135835.33/2203552· OSTI ID:2203552

Szink, Elizabeth ^[1]; Goff, Jennifer ^[2]; Durrence, Konnor ^[3]; Lui, Lauren ^[4]; Nielsen, Torben ^[4]; Kuehl, Jennifer ^[4]; Hunt, Kristopher ^[5]; Chandonia, John-Marc ^[4]; Thorgersen, Michael ^[3]; Poole, Farris ^[3]; Stahl, David ^[5]; Chakraborty, Romy ^[6]; Arkin, Adam ^[7]; Adams, Michael ^[3]

---

1. Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA; Oak Ridge National Laboratory
2. 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
3. Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
4. Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA
5. Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
6. Earth and Environmental Science Area, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA
7. Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA

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.

• Research Organization: U.S. Department of Energy Systems Biology Knowledgebase
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER)
• OSTI ID: 2203552
• Country of Publication: United States
• Language: English