Convergent host-parasite codon usage between honeybee and bee associated viral genomes

Journal of Invertebrate Pathology

Volumn 98, Issue 2, 2008, Pages 206-210

  Chantawannakul, Panuwan ^a   Cutler, Robert W ^b  

^a CHIANG MAI UNIVERSITY   (Thailand)

^b BARD COLLEGE   (United States)

Author keywords

Bee virus; Codon optimization; Genomics; Host parasite relationship

Indexed keywords

ANIMAL; ARTICLE; BEE; BEETLE; CODON; DROSOPHILA; GENETICS; GENOME; HOST PARASITE INTERACTION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOSQUITO; NUCLEOTIDE SEQUENCE; PICORNAVIRUS; VIROLOGY; VIRUS GENOME;

ANIMALS; BASE SEQUENCE; BEES; BEETLES; CODON; CULICIDAE; DROSOPHILA; EVOLUTION, MOLECULAR; GENOME, INSECT; GENOME, VIRAL; HOST-PARASITE INTERACTIONS; MOLECULAR SEQUENCE DATA; PICORNAVIRIDAE;

APIS MELLIFERA; APOIDEA; COLEOPTERA; HEXAPODA; RNA VIRUSES; TRIBOLIUM CASTANEUM;

EID: 43949113259     PISSN: 00222011     EISSN: 10960805     Source Type: Journal    
DOI: 10.1016/j.jip.2008.02.016     Document Type: Article

References (32)

1. Akashi H., and Eyre-Walker A. Translational selection and molecular evolution. Curr. Opin. Genet. Dev. 8 (1998) 688-693
2. Allen M.F., and Ball B.V. Characterization and serological relationships of strains of Kashmir bee virus. Ann. Appl. Biol. 126 (1995) 471-484
3. Ball B.V., and Allen M.F. The prevalence of pathogens in honeybee (Apis mellifera) colonies infested with the parasitic mite Varroa jacobsoni. Ann. Appl. Biol. 113 (1988) 237-244
4. Burge C., Campbell A.M., and Karlin S. Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci. USA 89 (1992) 1358-1362
5. Chen Y., Pettis J.S., and Feldlaufer M.F. Detection of multiple viruses in queens of the honeybee Apis mellifera L. J. Invert. Pathol. 90 (2005) 118-121
6. Cox-Foster D.L., Conlan S., Holmes E.C., Palacios G., Evans J.D., Moran N.A., Quan P., Briese T., Hornig M., Geiser D.M., Martinson V., Van Engelsdorp D., Kalkstein A.L., Drysdale A., Hui J., Zhai J., Cui L., Hutchison S.K., Simons J.F., Egholm M., Pettis J.S., and Lipkin W.I. A metagenomic survey of microbes in honeybee colony collapse disorder. Science (2007) 1146498
7. Cutler R.W., and Chantawannakul P. The effect of local nucleotides on synonymous codon usage in the honeybee (Apis mellifera L.) genome. J. Mol. Evol. 64 (2007) 637-645
8. De Miranda J.R., Drebot M., Tyler S., Shen M., Cameron C.E., Stoltz D.B., and Camazine S.M. Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus J. Gen. Virol. 85 (2004) 2263-2270
9. Frank A.C., and Lobry J.R. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238 (1999) 65-77
10. Freeman J.M., Plasterer T.N., Smith T.F., and Mohr S.C. Patterns of genome organization in bacteria. Science 279 (1996) 1827-1829
11. Fujiyuki T., Takeuchi H., Ono M., Ohka S., Sasaki T., Nomoto A., and Kubo T. Novel insect picorna-like virus identified in the brains of aggressive worker honeybees. J. Virol. 78 3 (2004) 1093-1100
12. Ghosh R.C., Ball B.V., Willcocks M.M., and Carter M.J. The nucleotide sequence of sacbrood virus of the honeybee: an insect picorna-like virus. J. Gen. Virol. 80 (1999) 1541-1549
13. Grantham R., Gautier C., Gouy M., Mercier R., and Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8 (1980) 49-62
14. Grosjean H., and Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed gene. Gene 18 (1982) 199-209
15. Govan V.A., Leat N., Allsopp M., and Davison S. Analysis of the complete genome sequence of acute bee paralysis virus shows that it belongs to the novel group of insect-infecting RNA viruses. Virology 277 2 (2000) 457-463
16. Honeybee genome sequencing consortium, 2006. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443, 931-949.
17. Jenkins G.M., Pagel M., Gould E.A., Zanotto P.M., and Holmes E.C. Evolution of base composition and codon usage bias in the genus flavivirus. J. Mol. Evol. 52 4 (2001) 383-390
18. Jernigan R.W., and Baran R.H. Pervasive properties of the genomic signature. BMC Genomics 3 (2002) 23-31
19. Jørgensen F.G., Schierup M.H., and Clark A.G. Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera. Mol. Biol. Evol. 24 2 (2007) 611-619
20. Karlin S., Blaisdell B.E., and Schachtel G.A. Contrasts in codon usage of latent versus productive genes of Epstein-Barr virus: data and hypotheses. J. Virol. 64 9 (1990) 4264-4273
21. Karlin S., Mrázek J., and Cambell A.M. Compositional biases of bacterial genomes and evolutionary implications. J. Bact. 179 12 (1997) 3899-3913
22. Karline S., Campbell A.M., and Mrázek J. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32 (1998) 185-225
23. Lobry J.R., and Sueoka N. Asymmetric directional mutational pressures in bacteria. Genome Biol. 3 10 (2002) 1-13
24. Macdónaill D.A., and Manktelow M. Molecular informatics: quantifying information patterns in the genetic code. Mol. Simul. 30 5 (2004) 267-272
25. Merkl R. A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency. J. Mol. Evol. 57 (2003) 453-466
26. Morton B.R. Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineage. J. Mol. Evol. 46 (1998) 449-459
27. Morton B.R., and So B.G. Codon usage in plastid gene is correlated with context, position within genes and amino acid content. J. Mol. Evol. 50 2 (2000) 184-193
28. Mrázek J., and Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl. Acad. Sci. USA 95 (1998) 3720-3725
29. Nordstom S., Fries I., Aarhus H., Hansen H., and Korpela S. Virus infection in Nordic honeybee colonies with no, low or severe Varroa jacobsoni infestations. Apidologie 33 (1999) 475-484
30. Ongus J.R., Peters D., Bengsch E., Vlak J.M., and van Oers M.M. Complete sequence of a picorna-like virus of the genus Iflavirus replicating in the mite Varroa destructor. J. Gen. Virol. 85 (2004) 3747-3755
31. Pride D.T., Wassenaar T.M., Ghos C., and Blaser M.J. Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses. BMC Genomics 7 (2006) 8
32. Sharp P.M., Stenico M., Peden J.F., and Lloyd A.T. Codon usage: mutational bias, translational selection, or both?. Biochem. Soc. Trans. 21 (1993) 835-841