IMG/M: integrated genome and metagenome comparative data analysis system

Abstract

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

“…3 and Supplementary Table 1). All GEBA-I genomes are publicly available through the Integrated Microbial Genomes with Microbiomes (IMG/M) system 15 and GenBank, and the corresponding strains through the respective culture collection (Supplementary Table 1).…”

“…Briefly, protein-coding genes (CDSs) were identified using Prodigal 59 followed by a round of automated and manual curation using the JGI GenePrimp pipeline 60 . Functional annotation and additional analyses were performed within the Integrated Microbial Genomes (IMG-ER) platform 15 . Genome completeness was estimated using the CheckM 14 genome quality estimator and individual CheckM completeness scores reported in Supplementary Table 1. Conserved single-copy gene phylogeny.…”

Complete genome sequence of Ruminococcaceae bacterium CPB6: A newly isolated culture for efficient n -caproic acid production from lactate

“…The PacBio sequencing generated 660.96-Mb data with 205-fold of coverage. Gene prediction and annotation were performed using the IMG/M system (Chen et al, 2017). The results of the annotation are summarized in Table 2, and a circular genome map is presented in Fig.…”

Draft Genome Sequences of Two Novel Sub-Antarctic Williamsia Species

“…However, strains 1135 and 1138 demonstrated 78.78% and 78.91% genetic similarities with W. muralis NBRC 105860 (Ga0128692) and 78.68% and 78.54% genetic similarities with Williamsia sp. D3 (Ga0041805), respectively, calculated using the average nucleotide identity (ANI) tool of IMG/M (7). A significant separation was also identified for both strains by principal-component analysis (PCA) using IMG/MER with all eight available Williamsia genomes; comparatively, the most closely related genomes were those of W. muralis and Williamsia sp.…”