Exploring the evolutionary dynamics of Rhizobium plasmids through bipartite network analysis
Xiangchen Li1,2, Hao Wang1,2, Wenjun Tong1
1State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Environmental Microbiology
|July 31, 2019
Summary
Network analysis reveals extensive plasmid diversity in Rhizobium bacteria. This study identifies 34 homologous plasmid clusters, including symbiotic and essential gene-carrying chromids, offering insights into bacterial evolution and adaptation.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Rhizobium bacteria possess a multipartite genome, including chromosomes and plasmids, making them ideal for plasmid biology research.
- Traditional phylogenetic methods have limitations in studying plasmid evolution due to a lack of universally shared genes.
Purpose of the Study:
- To conduct a comprehensive analysis of Rhizobium plasmids using network analysis.
- To explore the evolutionary relationships and diversity of plasmids within the Rhizobium genus.
Main Methods:
- Construction of a bipartite network connecting 216 Rhizobium plasmids and their homologous protein families.
- Application of hierarchical clustering to dissect the plasmid network and identify clusters.
- Analysis of network properties to infer plasmid variation and formation mechanisms.
Main Results:
- Identification of 34 distinct homologous plasmid clusters within Rhizobium.
- Discovery of four major clusters: one symbiotic plasmid cluster and two chromid clusters containing essential genes.
- Characterization of symbiotic and rare accessory clusters as exogenetic, contrasting with co-evolved common accessory clusters.
Conclusions:
- Rhizobium plasmids exhibit significant diversity and varied evolutionary trajectories.
- Network analysis provides a powerful approach to complement phylogenetics in studying bacterial plasmid evolution.
- Findings suggest mechanisms of plasmid variation including genetic exchange, fusion, fission, and adaptation to different lifestyles and environments.
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