U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


Database of DNA Viruses and Retroviruses Debuts on Integrated Microbial Genomes Platform
Published: October 13, 2016
Posted: December 28, 2016

Geographic distribution of biosamples and organisms encompassed by the Genomes OnLine Database. Organism location of isolation is marked with pink dots, biosample location with blue dots. [Image courtesy of Mukherjee et al., Nucleic Acids Research (2016). DOI: 10.1093/nar/gkw992]

The publicly accessible database promotes comparative analyses and ground-breaking discoveries through biological translation of sequence data.

The Science
A new database dedicated to global viral diversity has been developed by the Department of Energy Joint Genome Institute (DOE JGI). This database is the largest publicly available database for viruses, with 3,908 isolate reference DNA viruses and 264,413 computationally identified viral contigs from more than 6,000 ecologically diverse metagenomic samples. In a series of four articles recently published in Nucleic Acids Research, DOE JGI researchers also report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers.

The Impact
Microbes play key roles in maintaining the planet’s biogeochemical cycles. Viruses, thought to outnumber microbes by 10-fold, exert major influences on microbial survival and community interactions. Advances in sequencing technologies have generated vast amounts of data about these viruses, requiring tools to manage and interpret the information. Recent updates focus on database analytical tools for microbial genomics and viruses relevant to DOE missions in bioenergy and environment.

Summary
Providing high-quality, publicly accessible sequence data goes hand-in-hand with developing and maintaining the databases and tools that the research community can harness to help answer scientific questions. In a recent series of articles published in Nucleic Acids Research, researchers at DOE JGI, a national scientific user facility, describe a database called Integrated Microbial Genomes with Virus Samples (IMG/VR). IMG/VR is a comprehensive computational platform integrating all the sequences in the database with associated metadata and analytical tools. IMG/VR follows on the heels of a recent DOE JGI viral diversity study report in Nature. Additional articles in the same issue describe updates to several publicly accessible, interactive databases since the last set of reports published in 2014. For example, as of July 2016, there were 47,516 archaeal, bacterial, and eukaryotic genomes in the IMG with Microbiome Samples (IMG/M) system, with researchers noting that number “represents an over 300% increase since September 2013.” IMG/M contains annotated DNA and RNA sequence data of archaeal, bacterial, eukaryotic, and viral genomes from cultured organisms; single cell genomes (SCG) and genomes from metagenomes from uncultured archaea, bacteria, and viruses; and metagenomes from environmental, host-associated, and engineered microbiome samples. Another paper concerns the Genomes OnLine Database (GOLD), a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four-level classification system in the form of a study, organism (for isolates) or biosample (for environmental samples), sequencing project, and analysis project. A fourth paper focuses on the IMG Atlas of Biosynthetic gene Clusters (IMG-ABC). Launched in 2015, IMG-ABC enables researchers to search for biosynthetic gene clusters and secondary metabolites. Their latest update now incorporates ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across several thousand isolate microbial genomes, as well as a new search capability.

Contacts
Daniel Drell, Ph.D.
Program Manager
Biological Systems Science Division
Office of Biological and Environmental Research
Office of Science, U.S. Department of Energy
daniel.drell@science.doe.gov

Nikos Kyrpides
Prokaryote Super Program Head
DOE Joint Genome Institute
nckyrpides@lbl.gov

Funding
U. S. Department of Energy, Office of Science, Office of Biological and Environmental Research
U.S. National Institutes of Health Data Analysis and Coordination Center

Publications

I.-M. A. Chen, et al., “IMG/M: Integrated genome and metagenome comparative data analysis system.” Nucleic Acids Research (2016). [DOI:10.1093/nar/gkw929] (Reference link)

S. Mukherjee, et al., “Genomes OnLine Database (GOLD) v.6: Data updates and feature enhancements.” Nucleic Acids Research (2016). [DOI: 10.1093/nar/gkw992] (Reference link)

D. Paez-Espino, et al., “IMG/VR: A database of cultured and uncultured DNA Viruses and retroviruses.” Nucleic Acids Research (2016). [DOI: 10.1093/nar/gkw1030] (Reference link)

M. Hadjithomas, et al., “IMG-ABC: New features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.” Nucleic Acids Research (2016). [DOI: 10.1093/nar/gkw1103] (Reference link)

Related Links

IMG

GOLD

IMG/VR

IMG-ABC

JGI News Release: Unveiled: Earth's Viral Diversity

JGI Science Highlight: First Public Resource for Secondary Metabolites Searches

Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: DOE Joint Genome Institute (JGI)

Division: SC-23.2 Biological Systems Science Division, BER

 

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