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ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
Meng Liu1,2, Xiaobin Li1, Yingzhou Xie1
1State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.
Nucleic Acids Research
|November 9, 2018
Summary
ICEberg 2.0 is an updated database detailing bacterial integrative and conjugative elements (ICEs) and their interactions. The enhanced resource aids in understanding horizontal gene flow and predicting mobile genetic elements in bacterial genomes.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Bacterial integrative and conjugative elements (ICEs) are key drivers of horizontal gene transfer.
- Understanding ICEs and their interactions with mobilizable elements is crucial for microbial genomics.
Purpose of the Study:
- To update and expand the ICEberg database with comprehensive information on ICEs and related elements.
- To introduce new features for predicting ICEs and mobilizable elements in bacterial genomes.
Main Methods:
- Database update incorporating text mining and manual curation for ICE data.
- Inclusion of known transfer interactions between ICEs, integrative and mobilizable elements (IMEs), and cis-mobilizable elements (CIMEs).
- Development of the ICEfinder tool for predicting ICEs and IMEs using gene similarity and co-localization.
Main Results:
- ICEberg 2.0 now contains 1032 ICEs, including experimentally supported and predicted elements.
- Detailed transfer interactions involving 49 IMEs and 7 CIMEs with 19 ICEs are now available.
- Expanded collections of chromosome-borne IMEs (260) and CIMEs (235) have been added.
Conclusions:
- ICEberg 2.0 provides a significantly enhanced resource for studying bacterial ICEs.
- The database and prediction tool facilitate research into horizontal gene flow and microbial evolution.
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