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

Chen, I-Min A.; Markowitz, Victor; Chu, Ken; Palaniappan, Krishna; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Andersen, Evan; Huntemann, Marcel; Varghese, Neha; Hadjithomas, Michalis; Tennessen, Kristin; Nielsen, Torben; Ivanova, Natalia; Kyrpides, Nikos C.

doi:10.1093/nar/gkw929

Cited by 426 publications

(427 citation statements)

References 39 publications

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“…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).…”

Section: R E S O U R C Ementioning

confidence: 99%

“…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.…”

Section: Competing Financial Interestsmentioning

confidence: 99%

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

et al. 2017

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We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

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Section: R E S O U R C Ementioning

confidence: 99%

Section: Competing Financial Interestsmentioning

confidence: 99%

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

et al. 2017

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“…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.…”

mentioning

confidence: 99%

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

Tao

Zhu

Wang

et al. 2017

Journal of Biotechnology

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“…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.…”

Section: Genome Announcementmentioning

confidence: 99%