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Updated: Jun 28, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Multiple genome alignment for identifying the core structure among moderately related microbial genomes
1Department of Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan. uchiyama@nibb.ac.jp
BMC Genomics
|November 4, 2008
Summary
Identifying the genomic core in prokaryotes is challenging due to gene transfer. This study developed a robust method using conserved gene order to define the core genome, improving accuracy over simpler methods.
Area of Science:
- Genomics
- Comparative Genomics
- Bioinformatics
Background:
- Horizontal gene transfer complicates identifying conserved genes in prokaryotes.
- Core genome identification is difficult for distantly related genomes.
- Conserved gene order suggests vertical inheritance and aids in defining the core genome.
Purpose of the Study:
- To develop and apply a method for identifying the genomic core based on conserved gene order.
- To define the core structure as segments with conserved gene order, indicating vertical inheritance.
Main Methods:
- Developed a method to identify core genome structure by finding orthologous group orders that maximize conserved gene order.
- Applied the method to Bacillaceae and Enterobacteriaceae families.
Main Results:
- Identified core structures of 1438 and 2125 orthologous groups (OGs) for Bacillaceae and Enterobacteriaceae, respectively.
- The core sets included essential genes; the intersection comprised ~700 OGs.
- Gene order conservation provided a more robust genomic core definition than gene conservation alone.
- Core genes showed higher G+C homogeneity and phylogenetic congruence, indicating indigenous origin and shared evolutionary history.
Conclusions:
- Genome alignment based on gene order conservation is effective for identifying the genomic core in moderately related microbial genomes.
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