Turn a novel genome sequence into a reproducible, publication quality Genome Announcement.
Jul 24, 2020

A New Way to Share Novel Genomes

The Science

Many scientists find value in isolating microorganisms and sequencing their genomes, one at a time. Others take an environmental sample and sequence all the organisms inside at once. Then, researchers use advanced computing to piece individual genomes back together. While a single genome isn’t viewed as cutting edge science today, discoveries that occur when comparing genomes can be. Modeling how organisms, especially novel lineages, interact with their environment is important for understanding how they adapt and evolve. KBase is a knowledge creation and discovery environment for systems biology that enables sharing and collaboration. We are working with the community to accelerate discoveries across biological systems, one genome at a time.

The Impact

Using KBase for genome analysis, researchers can rapidly generate and publish results. KBase accepts raw genomic sequence data and provides a variety of analysis tools. The results can easily be shared in a concise and reproducible framework that follows the FAIR data principles – findable, accessible, interoperable, and reusable. Genome analyses provided by KBase are compatible with several journal publications, including Microbiome Research Announcements, Genome Biology and Evolution, Journal of Genomics, and 3biotech.

Representation of the NCBI RefSeq genome for Vibrio cholerae MJ-1236 chromosome 1 (NC_012668)


Example data visualization output from the Circular Genome Visualization Tool in KBase. This is a representation of the NCBI RefSeq genome for Vibrio cholerae MJ-1236 chromosome 1 (NC_012668).

Summary

Four soil bacterium genomes were isolated from roots associated with poplar trees growing in the Southern USA. One of the genomes was closely related to a bacterium isolated from semiarid savannah soil in Namibia (Terriglobus albidus strain ORNL). Another genome (Larkinella sp. Strain BK230) had only 5 related isolates previously identified and sequenced. A third (Starkeya sp. Strain ORNL1) was closely related to strains that were identified in soil samples from the 1930s. The last strain (Roseimicrobium sp. Strain ORNL1) was most closely related to a bacterium isolated from a soil sample in Japan. With these new genomes available in KBase, researchers can begin to identify genes associated with the evolution of plant-microbe interactions. All four genomes with complete analyses are publicly available inside KBase. Any KBase user can explore these data, add their own, or run new analyses. They are also available as public Narratives for review outside the KBase login.

These are just a few examples of published genome announcements enabled by analysis in KBase. KBase tools were used to check the quality of the genome sequence, and to build models of the metabolic potential of these bacteria based on the genetic information encoded in the genome. Many more examples of published genome announcements with analyses done in KBase can be found here. Please contact us at engage@kbase.us to learn more about using KBase for your research.

Publications

D.A. Pelletier, et al. (Plant Microbe Interfaces Science Focus Area) “Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides RootsMicrobiology Resource Announcements 9(12), e00159-20 (2020). [DOI: 10.1128/MRA.00159-20]

Podar, et al. ((Plant Microbe Interfaces Science Focus Area) “Complete Genome Sequence of Terriglobus albidus Strain ORNL, an Acidobacterium Isolated from the Populus deltoides RhizosphereMicrobiology Resource Announcements 8(46), e01065-19 (2019). [DOI: 10.1128/MRA.01065-19]

Podar, et al. (Plant Microbe Interfaces Science Focus Area) “Complete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides Rhizosphere” Microbiology Resource Announcements 9(27), e00617-20 (2020). [DOI: 10.1128/MRA.00617-20]

Podar, et al. (Plant Microbe Interfaces Science Focus Area) “Complete Genome Sequence of Starkeya sp. Strain ORNL1, a Soil Alphaproteobacterium Isolated from the Rhizosphere of Populus deltoidesMicrobiology Resource Announcements 9(27), e00644-20 (2020). [DOI: 10.1128/MRA.00644-20]

Related Links

Make the Most Out of Genome Announcements with KBase, KBase Newsletter (April 2020)

DOI: 10.25982/1608940

Funding

DOE Systems Biology Knowledgebase (KBase) is funded by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886. 

The highlighted research by the ORNL team was funded by the U.S. DOE Office of Biological and Environmental Research, Genomic Science Program as part of the Plant Microbe Interfaces ScientificFocus Area (http://pmi.ornl.gov). Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.

Elisha Wood-Charlson
Elisha Wood-Charlson | Engagement Lead
Lawrence Berkelely National Laboratory

Elisha M Wood-Charlson is KBase’s User Engagement Lead. She has a PhD and 10+ years of experience as a microbial ecologist focused on host-microbe-virus interactions in the marine environment. Since leaving the research bench, she has moved into the realm of scientific community engagement, with the goal of making microbiome data science more efficient through effective collaboration, building trust in online communities, and developing shared ownership throughout the scientific process.