Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family

Australian Journal of Botany

Volumn 60, Issue 5, 2012, Pages 461-470

  Zhang, Yuerong ^a   Nie, Xiaojun ^a   Jia, Xiaoou ^a   Zhao, Cunzhen ^a   Biradar, Siddanagouda S ^a   Wang, Le ^a   Du, Xianghong ^a   Weining, Song ^a  

^a NORTHWEST A F UNIVERSITY   (China)

Author keywords

mutational bias; optimal codon

Indexed keywords

CHLOROPLAST; CORRESPONDENCE ANALYSIS; GENE EXPRESSION; GENOME; MONOCOTYLEDON; MUTATION; NATURAL SELECTION; TRAJECTORY;

EID: 84865205879     PISSN: 00671924     EISSN: None     Source Type: Journal    
DOI: 10.1071/BT12073     Document Type: Article

References (41)

1. Bellgard M, Schibeci D, Trifonov E, Gojobori T (2001) Early detection of G+C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. Journal of Molecular Evolution 53, 465-468. doi:10.1007/s002390010236
2. Blake WJ, Kaern M, Cantor CR, Collins JJ (2003) Noise in eukaryotic gene expression. Nature 422, 633-637. doi:10.1038/nature01546
3. CampbellWH,GowriG(1990)Codonusage in higher plants, green algae, and cyanobacteria. Plant Physiology 92, 1-11. doi:10.1104/pp.92.1.1
4. Carels N, Bernardi G (2000) Two classes of genes in plants. Genetics 154, 1819-1825.
5. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nature Genetics 31, 415-418.
6. Duret L, Mouchiroud D (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 96, 4482-4487. doi:10.1073/pnas.96.8.4482
7. Eyre-Walker A (1996) Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy? Molecular Biology and Evolution 13, 864-872. doi:10.1093/oxfordjournals.molbev.a025646
8. Gielly L, Taberlet P (1994) The use of chloroplast DNA to resolve plant phylogeny: noncoding versus rbcL sequences. Molecular Biology and Evolution 11, 769-777.
9. Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Research 10, 7055-7074. doi:10.1093/nar/10.22.7055
10. Grantham R, Gautier C, GouyM(1980) Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Research 8, 1893-1912. doi:10.1093/nar/8.9.1893
11. Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Research 9, 213. doi:10.1093/nar/9.1.213-b
12. Gupta SK, Bhattacharyya TK, GhoshTC (2004) Synonymous codon usage in Lactococcus lactis: mutational bias versus translational selection. Journal of Biomolecular Structure & Dynamics 21, 527-535. doi:10.1080/07391102.2004. 10506946
13. Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS ONE 6, e19254. doi:10.1371/journal.pone.0019254
14. Hou ZC, Yang N (2000) Analysis of factors shaping S. pneumoniae codon usage. Acta Genetica Sinica 29, 747-752.
15. Howe CJ, Barbrook AC, Koumandou VL, Nisbet RE, Symington HA (2003) Evolution of the chloroplast genome. Philosophical Transactions of the Royal Society B Biological Sciences 358, 99-107. doi:10.1098/rstb.2002.1176
16. Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution 2, 13-34.
17. Jia J, Xue Q (2009) Codon usage biases of transposable elements and host nuclear genes in Arabidopsis thaliana and Oryza sativa. Genomics, Proteomics & Bioinformatics 7, 175-184. doi:10.1016/S1672-0229(08)60047-9
18. Kawabe A, Miyashita NT (2003) Patterns of codon usage bias in three dicot and four monocot plant species. Genes & Genetic Systems 78, 343-352. doi:10.1266/ggs.78.343
19. Le Z, Jin LG, Luo L, Wang YP, Dong ZM, Sun SH, Qiu LJ (2011) Analysis of nuclear gene codon bias on soybean genome and transcriptome. Acta Agronomica Sinica 37, 965-974. doi:10.3724/SP.J.1006.2011.00965
20. Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos MR, D'Hont A, Garsmeur O, Vilarinhos AD, Kanamori H, Matsumoto T, Ronning CM, Cheung F, Haas BJ, Althoff R, Arbogast T, Hine E, Pappas GJ, Sasaki T, Souza MT, Miller R, Glaszmann JC, Town CD (2008) Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 9, 58. doi:10.1186/1471-2164-9-58
21. Liu QP (2006) Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans. Bio Systems 85, 99-106. doi:10.1016/j. biosystems.2005.12.003
22. Liu QP, Xue QZ (2005) Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. Journal of Genetics 84, 55-62. doi:10.1007/BF02715890
23. Lu H, Zhao WM, Zheng Y, Wang H, Qi M, Yu XP (2005) Analysis of synonymous codon usage bias in Chlamydia. Acta Biochimica et Biophysica Sinica 37, 1-10. doi:10.1093/abbs/37.1.1
24. Lynn DJ, Singer GA, Hickey DA(2002) Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Research USA 30, 4272-4277. doi:10.1093/nar/gkf546
25. McInerney JO (1998) Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proceedings of the National Academy of Sciences of the United States of America 95, 10698-10703. doi:10.1073/pnas.95.18.10698
26. Rosenberg MS, Subramanian S, Kumar S (2003) Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution 20, 988-993. doi:10.1093/molbev/msg113
27. Sablok G, Nayak KC, Vazquez F, Tatarinova TV (2011) Synonymous codon usage, GC3, and evolutionary patterns across plastomes of three pooid model species: emerging grass genome models for monocots. Molecular Biotechnology 49, 116-128. doi:10.1007/s12033-011-9383-9
28. Sharp PM, Li WH (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research 15, 1281-1295. doi:10.1093/nar/15.3.1281
29. Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F (1988) Codon usage in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Research 16, 8207-8211. doi:10.1093/nar/16.17.8207
30. Sharp PM, Emery LR, Zeng K (2010) Forces that influence the evolution of codon bias. Philosophical Transactions of the Royal Society Biological Sciences 365, 1203-1212. doi:10.1098/rstb.2009.0305
31. Shaw J, Lickey EB, Beck JT, Farmer SS, Liu W, Miller J, Chaw SK, Winder CT, Schilling EE, Small RL (2005) The tortoise and the hare: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92, 142-166. doi:10.3732/ajb.92.1.142
32. Sueoka N (1962) On the genetic basis of variation and heterogeneity of DNA base composition. Proceedings of the National Academy of Sciences of the United States of America 48, 582-592. doi:10.1073/pnas.48.4.582
33. Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proceedings of the National Academy of Sciences of the United States of America 85, 2653-2657. doi:10.1073/pnas.85.8.2653
34. Sueoka N (1999) Translation-coupled violation of parity rule human genes is not the case of heterogeneity of the DNA G+C content of third codon position. Gene 238, 53-58. doi:10.1016/S0378-1119(99)00320-0
35. Sueoka N, KawanishiY(2000)DNAG+Ccontent of the third codon position and codon usage biases of human genes. Gene 261, 53-62. doi:10.1016/S0378-1119(00) 00480-7
36. Sugiura M (1992) The chloroplast genome. Plant Molecular Biology 19, 149-168. doi:10.1007/BF00015612
37. Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA (2010) GC3 biology in corn, rice, sorghum and other grasses.BMCGenomics 11, 308. doi:10.1186/1471- 2164-11-308
38. Wan XF, Xu D, Kleinhofs A, Zhou JZ (2004) Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evolutionary Biology 4, 19. doi:10.1186/1471-2148-4-19
39. Wang B, Yuan J, Liu J, Jin L, Chen JQ (2011) Codon usage bias and determining forces in green plant mitochondrial genomes. Journal of Integrative Plant Biology 53, 324-334. doi:10.1111/j.1744-7909.2011.01033.x
40. Wright F (1990) The 'effective number of codons' used in a gene. Gene 87, 23-29. doi:10.1016/0378-1119(90)90491-9
41. Xia X (1998) How optimized is the translational machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae? Genetics 149, 37-44.