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Research Article Open access CC BY 4.0

Relationship of Genomic G+C Content between Phages/Plasmids and Their Hosts

Hiroshi Nakashima, Keiko Homma, Kazuhiro Mawatari

Biotechnology Journal International · pp. 1–9 · Published 19 Aug 2015

10.9734/BBJ/2015/20046

Abstract

Aims: We compared genomic G+C content between bacteriophages/plasmids and their host genomes of 46 species to reveal their relation. To examine the large deviation in the G+C content between bacteriophages and their host genomes, the ancestral bacteriophage which infected early was estimated using homologous genes of bacteriophages based on G+C content at the third codon positions. Place and Duration of Study: Department of Clinical Laboratory Science, Graduate Course of Medical Science and Technology, School of Health Sciences, Kanazawa University, Japan. Methodology: The bacteria employed in this study consist of 6 species from Archaea and 40 species from Eubacteria. Orthologs were identified by the two-directional best hit approach of homology search. A phylogenetic tree was obtained by multiple sequence alignment of homologous genes. The ancestral bacteriophage which infected early was estimated based on G+C content at the third codon positions. We assumed that the two bacteriophages have evolved from a common ancestor, and their identical codons were thought to represent their ancestor type. Results: The relationship of G+C content between bacteriophages/plasmids and host genomes was almost linear. Three bacteriophages were largely deviated from the linear relation. A phylogenetic tree obtained using the orthologs of Mycobacterium smegmatis indicated which bacteriophage branched early. Assuming that the G+C content of identical codons represents their common ancestor, the ancestor was estimated that it had similar G+C content with its host.

Genomic G C content bacteriophage and plasmid G C content deviation G C content at the third codon positions

References (26)

  1. 1 Basic Local Alignment Search Tool [DOI]
  2. 2 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice [DOI]
  3. 3 Lateral gene transfer and the nature of bacterial innovation [DOI]
  4. 4 Virioplankton: Viruses in Aquatic Ecosystems [DOI]
  5. 5 DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae [DOI]
  6. 6 The KEGG databases at GenomeNet [DOI]
  7. 7 Amelioration of Bacterial Genomes: Rates of Change and Exchange [DOI]
  8. 8 Dinucleotide relative abundance extremes: a genomic signature [DOI]
  9. 9 The guanine and cytosine content of genomic DNA and bacterial evolution. [DOI]
  10. 10 Base composition bias might result from competition for metabolic resources [DOI]
  11. 11 Compositional biases of bacterial genomes and evolutionary implications [DOI]
  12. 12 The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages [DOI]
  13. 13 Examining bacterial species under the specter of gene transfer and exchange [DOI]
  14. 14 On the nature of mycobacteriophage diversity and host preference [DOI]
  15. 15 The UCSC Archaeal Genome Browser: 2012 update [DOI]
  16. 16 Evidence for horizontal gene transfer in Escherichia coli speciation [DOI]
  17. 17 Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. [DOI]
  18. 18 Comparative Genomic Analysis of 18 Pseudomonas aeruginosa Bacteriophages [DOI]
  19. 19 Horizontal gene transfer and bacterial diversity [DOI]
  20. 20 COMPOSITION OF THE DESOXYPENTOSE NUCLEIC ACIDS OF FOUR GENERA OF SEA-URCHIN [DOI]
  21. 21 A test of Chargaff’s second rule [DOI]
  22. 22 Comparative Analyses of Base Compositions, DNA Sizes, and Dinucleotide Frequency Profiles in Archaeal and Bacterial Chromosomes and Plasmids [DOI]
  23. 23 Seapration of B. subtilis DNA into complementary strands. II. Template functions and composition as determined by transcription with RNA polymerase. [DOI]
  24. 24 Genes from Nine Genomes Are Separated into Their Organisms in the Dinucleotide Composition Space [DOI]
  25. 25 The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions [DOI]
  26. 26 Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content [DOI]

Cited by 3

Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR

Na L. Gao, Jingchao Chen, Teng Wang · bioRxiv · 2018

Prokaryotic genome expansion is facilitated by phages and plasmids but impaired by CRISPR

Na L. Gao, Jingchao Chen, Martin J Lercher · 2018

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