Faster, Bigger, Stronger: Genome Database Improvements

The Science

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.

Summary

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.

BER Program Manager

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]

References

Markowitz, V. M., I-M. A. Chen, K. Chu, E. Szeto, K. Palaniappan, M. Pillay, A. Ratner, J. Huang, T. Woyke, M. Huntemann, I. Anderson, K. Billis, N. Varghese, K. Mavromatis, A. Pati, N. N. Ivanov, N. C. Kyrpides. 2013. “IMG 4 Version of the Integrated Microbial Genomes Comparative Analysis System,” Nucleic Acids Research 42(D1), D560–67. DOI:10.1093/nar/gkt963.

Markowitz, V. M., I-M. A. Chen, K. Chu, E. Szeto, K. Palaniappan, M. Pillay, A. Ratner, J. Huang, I. Pagani, S. Tringe, M. Huntermann, K. Billis, N. Varghese, K. Tennessen, K. Mavromatis, A. Pati, N. N. Ivanova, N. C. Kyrpides. 2013. “IMG/M 4 Version of the Integrated Metagenome Comparative Analysis System,” Nucleic Acids Research 42 (D1), D568–73. DOI:10.1093/nar/gkt919.