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Evolutionary dynamics of overlapped genes in Salmonella
Yingqin Luo1, Fabia Battistuzzi, Kui Lin
1Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America ; Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.
Plos One
|December 7, 2013
Summary
Overlapping genes (OGs) in Salmonella are more likely to be conserved within operons than outside them. Gene loss is more frequent when OGs within operons separate, suggesting co-regulation influences their evolutionary fate.
Area of Science:
- Genomics
- Evolutionary Biology
- Microbial Genetics
Background:
- Overlapping genes (OGs) are common in bacterial genomes, sharing coding sequences and often exhibiting co-regulation.
- The evolutionary dynamics of OGs, including disruption and gene loss, are crucial for understanding genome evolution and gene function.
Purpose of the Study:
- To investigate the evolutionary patterns and disruption rates of ancestrally overlapping genes in 15 Salmonella strains.
- To determine how gene overlap is conserved or disrupted within and outside of operons.
- To explore the role of co-regulation in the fate of overlapping genes.
Main Methods:
- Comparative genomics analysis of 15 Salmonella species genomes.
- Phylogenetic analysis to reconstruct ancestral gene states.
- Examination of overlapping gene fates within and outside of operons.
Main Results:
- Overlapping genes within operons show higher conservation rates (0.89) compared to those outside operons (0.83).
- Separated overlapping genes within operons experience higher partner gene loss (0.02) than those outside operons (0.01).
- A significant majority of OG disruptions occurred before the common ancestor of the studied Salmonella strains, allowing for Salmonella-E. coli disruption estimates.
Conclusions:
- Co-regulation significantly influences the evolutionary trajectories of overlapping genes.
- Operon structure plays a distinct role in the conservation and disruption of overlapping genes.
- Most overlapping gene disruptions in Salmonella predate their common ancestor.
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