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

BER Research Highlights


Faster, Bigger, Stronger: Genome Database Improvements
Published: October 27, 2013
Posted: February 12, 2014

The Department of Energy’s Joint Genome Institute (DOE JGI) maintains the Integrated Microbial Genomes (IMG) data warehouse, which contains a rich collection of genomes from all three domains of life. IMG/M provides a similar collection of partially assembled genome reads from microbial communities (metagenomes). Both have recently been upgraded to address the increase in genome sequences and provide more options for users. IMG was introduced in 2005. Since the last published report in 2012, both systems have grown and improved. The improvements for both systems are described in a pair of reports in the Jan. 1, 2014, issue of Nucleic Acids Research.

The late 2013 version of IMG contains more than 16,000 genome datasets with more than 42 million protein-coding genes. Most (nearly 12,000) are bacterial, archaeal, and eukaryotic genomes. The number of genomes is more than three times the number two years ago. IMG also includes thousands of viral genomes, plasmids that did not come from a specific microbial genome sequencing project, and hundreds of genome fragments. Also in late 2013, IMG/M contained 3,328 metagenome datasets from 460 metagenome studies, with more than 19.5 billion protein coding genes.

Both systems have enhanced analysis tools for publicly available datasets. The latest version of IMG includes tools for recording and analyzing single cell genomes, RNA sequencing data, and gene clusters coding for synthesis of complex organic molecules (biosynthetic clusters).
Both systems are continually being improved to keep up with recent advances in genomics. Future advances will include incorporating pangenomic data (genes that make up the core genes common to all individuals in a species as well as variant genes to enable some individuals to adapt to different environments) and analysis tools for IMG and metaproteomics datasets (protein samples collected from environmental sources) in IMG/M.

References: Markowitz, V. M., et al. 2013. “IMG 4 Version of the Integrated Microbial Genomes Comparative Analysis System,” Nucleic Acids Research 42(D1), D560–67. DOI:10.1093/nar/gkt963. (Reference link)

Markowitz, V. M., et al. 2013. “IMG/M 4 Version of the Integrated Metagenome Comparative Analysis System,” Nucleic Acids Research 42 (D1), D568–73. DOI:10.1093/nar/gkt919. (Reference link)

Related Links:
IMG website: https://img.jgi.doe.gov/
IMG/M website: https://img.jgi.doe.gov/cgi-bin/m/main.cgi

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: Computational Biology, Bioinformatics, Modeling

Division: SC-23.2 Biological Systems Science Division, BER

 

BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Aug 24, 2019
New Approach for Studying How Microbes Influence Their Environment
A diverse group of scientists suggests a common framework and targeting of known microbial processes [more...]

Aug 08, 2019
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures. [more...]

Aug 05, 2019
Amazon Forest Response to CO2 Fertilization Dependent on Plant Phosphorus Acquisition
AmazonFACE Model Intercomparison. The Science Plant growth is dependent on the availabi [more...]

Jul 29, 2019
A Slippery Slope: Soil Carbon Destabilization
Carbon gain or loss depends on the balance between competing biological, chemical, and physical reac [more...]

Jul 15, 2019
Field Evaluation of Gas Analyzers for Measuring Ecosystem Fluxes
How gas analyzer type and correction method impact measured fluxes. The Science A side- [more...]

List all highlights (possible long download time)