ArticleBMC genomics2008
Multiple genome alignment for identifying the core structure among moderately related microbial genomes.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Comparative genomic analysis of poly-γ-glutamic acid producing Bacillus licheniformis strains isolated from dairy products.Journal, genetic engineering & biotechnology · 2026Article
- Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Comprehensive genomic analysis ofComputational and structural biotechnology journal · 2023Article
- The physiological potential of anammox bacteria as revealed by their core genome structure.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons.Nucleic acids research · 2019Article
- Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation.BMC genomics · 2018Article
- An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil.The ISME journal · 2017Article
- Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands.PloS one · 2016Article
- Chromosome painting in silico in a bacterial species reveals fine population structure.Molecular biology and evolution · 2013Article
- Genomic Basis for Methicillin Resistance in Staphylococcus aureus.Infection & chemotherapy · 2013Review
- MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.Nucleic acids research · 2013Article
- Evaluation method for the potential functionome harbored in the genome and metagenome.BMC genomics · 2012Article
- The core and unique proteins of haloarchaea.BMC genomics · 2012Article
- Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species.Genome biology and evolution · 2012Article
- Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes.BMC microbiology · 2011Article
- Save the tree of life or get lost in the woods.Biology direct · 2010Article
- Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins.BMC genomics · 2010Article
- Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics.BMC genomics · 2010Article
- Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter.Genome research · 2009Article
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1 author.
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Abstract
backgroundIdentifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders.
resultsThe method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes.
conclusionThe results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.
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