IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase
IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase
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DOI：
10.1093/nar/gkz932
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Mouncey, Nigel J.
中科院分区：
文献类型：
--
作者：
Palaniappan, Krishnaveni;Chen, I-Min A.;Mouncey, Nigel J.
微生物次生代谢是具有巨大生物技术和生物医学潜力的生物活性化合物的库。负责产生这些次级代谢物 (SM)（也称为天然产物）的生物合成机制通常由称为生物合成基因簇 (BGC) 的并置基因组编码。分离株和宏基因组样本的高通量基因组测序与专门计算工作流程的开发相结合，使得 BGC 的系统鉴定和新型 SM 的发现成为可能。为了推进微生物次生代谢及其多样性的探索，我们开发了最大的预测 BGC 与实验验证的 BGC 相结合的公开数据库，即生物合成基因簇综合微生物基因组图谱 (IMG-ABC) (https://img.jgi.doe.gov/abc-public)。在这里，我们描述了 IMG-ABC 知识库自 2015 年首次发布以来的第一次主要内容更新，使用最新版本的 antiSMASH (v5) 刷新了 BGC 预测管道，并在来自 GOLD (https://gold.jgi.doe.gov/) 的基础环境元数据背景下呈现数据。与之前的版本相比，本次更新大大提高了预测BGC的质量并扩展了预测的BGC类型。
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). 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 meta-data 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.