IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase

Palaniappan, Krishnaveni; Chen, I-Min A.; Chu, Ken; Ratner, Anna; Seshadri, Rekha; Kyrpides, Nikos C.; Ivanova, Natalia N.; Mouncey, Nigel J.

doi:10.1093/nar/gkz932

Title: IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase

Journal Article · Tue Oct 29 00:00:00 EDT 2019 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkz932· OSTI ID:1661596

Palaniappan, Krishnaveni ^[1]; Chen, I-Min A. ^[1]; Chu, Ken ^[1]; Ratner, Anna ^[1]; Seshadri, Rekha ^[1]; Kyrpides, Nikos C. ^[1]; Ivanova, Natalia N. ^[1]; Mouncey, Nigel J. ^[1]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division

Microbial secondary metabolism is a reservoir of bioactive compounds of immense biotechnological and biomedical potential. The biosynthetic machinery responsible for the production of these secondary metabolites (SMs) (also called natural products) is often encoded by collocated groups of genes called biosynthetic gene clusters (BGCs). Here, high-throughput genome sequencing of both isolates and metagenomic samples combined with the development of specialized computational workflows is enabling systematic identification of BGCs and the discovery of novel SMs. In order to advance exploration of microbial secondary metabolism and its diversity, we developed the largest publicly available database of predicted BGCs combined with experimentally verified BGCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc-public). Here we describe the first major content update of the IMG-ABC knowledgebase, since its initial release in 2015, refreshing the BGC prediction pipeline with the latest version of antiSMASH (v5) as well as presenting the data in the context of underlying environmental metadata sourced from GOLD (https://gold.jgi.doe.gov/). This update has greatly improved the quality and expanded the types of predicted BGCs compared to the previous version.

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Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1661596

Journal Information:: Nucleic Acids Research, Vol. 48, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 52 works

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