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

Abstract

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.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
  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
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1661596
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 48; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Palaniappan, Krishnaveni, Chen, I-Min A., Chu, Ken, Ratner, Anna, Seshadri, Rekha, Kyrpides, Nikos C., Ivanova, Natalia N., and Mouncey, Nigel J. IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. United States: N. p., 2019. Web. doi:10.1093/nar/gkz932.
Palaniappan, Krishnaveni, Chen, I-Min A., Chu, Ken, Ratner, Anna, Seshadri, Rekha, Kyrpides, Nikos C., Ivanova, Natalia N., & Mouncey, Nigel J. IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. United States. https://doi.org/10.1093/nar/gkz932
Palaniappan, Krishnaveni, Chen, I-Min A., Chu, Ken, Ratner, Anna, Seshadri, Rekha, Kyrpides, Nikos C., Ivanova, Natalia N., and Mouncey, Nigel J. Tue . "IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase". United States. https://doi.org/10.1093/nar/gkz932. https://www.osti.gov/servlets/purl/1661596.
@article{osti_1661596,
title = {IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase},
author = {Palaniappan, Krishnaveni and Chen, I-Min A. and Chu, Ken and Ratner, Anna and Seshadri, Rekha and Kyrpides, Nikos C. and Ivanova, Natalia N. and Mouncey, Nigel J.},
abstractNote = {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.},
doi = {10.1093/nar/gkz932},
journal = {Nucleic Acids Research},
number = D1,
volume = 48,
place = {United States},
year = {Tue Oct 29 00:00:00 EDT 2019},
month = {Tue Oct 29 00:00:00 EDT 2019}
}

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