Comparison of base composition and codon usage in insect mitochondrial genomes

Genes and Genomics

Volumn 31, Issue 1, 2009, Pages 65-71

  Sun, Zheng ^a   Wan, Dong Guang ^a   Murphy, Robert W ^b,c   Liang, Ma ^d   Zhang, Xian Sheng ^a   Huang, Da Wei ^a,d  

^a SHANDONG AGRICULTURAL UNIVERSITY   (China)

^b DEPARTMENT OF NATURAL HISTORY   (Canada)

^c KUNMING INSTITUTE OF ZOOLOGY   (China)

^d INSTITUTE OF ZOOLOGY   (China)

Author keywords

Codon usage; Insect mitochondrial genome; Non optimal codon anti codon usage; tRNA anticodon

Indexed keywords

CALLIPHORIDAE; COCHLIOMYIA HOMINIVORAX; DIPTERA; HEXAPODA; HYMENOPTERA; LEPIDOPTERA; VERTEBRATA;

EID: 63149144491     PISSN: 19769571     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF03191139     Document Type: Article

References (26)

1. Abascal F, Posada D, Knight RD and Zardoya R (2006) Parallel evolution of the genetic code in Arthropod mitochondrial genomes. PLoS Biol 4- e127.
2. Agris PF (2004) Decoding the genome: a modified view. Nucleic Acids Res. 32: 223-238.
3. Akashi H (2003) Translational selection and yeast proteome evolution. Genetics 164: 1291-1303.
4. Bulmer M (1987) Coevolution of codon usage and transfer RNA abundance. Nature 325: 728-730.
5. Crick FHC (1966) Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19: 548-555.
6. Crozier RH and Crozier YC (1993) The Mitochondrial Genome of the Honeybee Apis mellifera: Complete Sequence and Genome Organization. Genetics 133: 97-117.
7. Feijao PC, Neiva LS, Azeredo-Espin AMLd and Lessinger AC (2006) AMiGA: the arthropodan mitochondrial genomes accessible database. Bioinformatics: btl021.
8. Gibson A, Gowri-Shankar V, Higgs PG and Rattray M (2005) A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Molecular Biology and Evolution 22: 251-264.
9. Jia W and Higgs PG (2008) Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol. Biol. Evol. 25: 339-351.
10. Kamatani T and Yamamoto T (2007) Comparison of codon usage and tRNAs in mitochondrial genomes of Candida species. Biosystems 90: 362-370.
11. Lavner Y and Kotlar D (2005) Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 345: 127-138.
12. Lessinger AC, Martins Junqueira AC, Lemos TA, Kemper EL, da Silva FR, Vettore AL, Arruda P and L and Azeredo-Espin AM (2000) The mitochondrial genome of the primary screwworm fly Cochliomyia hominivorax (Diptera: Calliphoridae). Insect Mol. Biol. 9: 521-529.
13. Mclnerney JO (2006) The causes of protein evolutionary rate variation. Trends Ecol. Evol. 21: 230-232.
14. Moriyama EN and Powell JR (1997) Codon usage bias and tRNA abundance in Drosophila. J. Mol. Evol. 45: 514-523.
15. Rocha EPC (2004) Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 14: 2279-2286.
16. Sakurai M, Ohtsuki T, Suzuki T and Watanabe K (2005) Unusual usage of wobble modifications in mitochondrial tRNAs of the nematode Ascaris suum. FEBS Letters 579: 2767-2772.
17. Santos MAS, Moura G, Massey SE and Tuite MF (2004) Driving change: the evolution of alternative genetic codes. Trends Genet. 20: 95-102.
18. Sharp PM, Tuohy TMF and Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14: 5125-5143.
19. Tomita K, Ueda T and Watanabe K (1999) The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Res. 27: 1683-1689.
20. Vernon D, Gutell RR, Cannone JJ, Rumpf RW and William Birky C Jr. (2001) Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma. Mol. Biol. Evol. 18: 1810-1822.
21. Wolstenholme DR and Clary DO (1985) Sequence evolution of Drosophila mitochondrial DNA. Genetics 109: 725-744.
22. Xia X (1996) Maximizing Transcription Efficiency Causes Codon Usage Bias. Genetics 144: 1309-1320.
23. Xia X (2005) Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes. Gene 345: 13-20.
24. Xia X (2007) An improved implementation of codon adaptation index. Evol. Bioinformatics 3: 53-58.
25. Xia X and Xie Z (2001) DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92: 371-373.
26. Yokobori SH, Suzuki T and Watanabe K (2001) Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity. J. Mol. Evol. 53: 314-326.