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Rapid Communications

Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes

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Pages 2500-2506 | Received 15 Apr 2020, Accepted 06 Jun 2020, Published online: 17 Jun 2020

References

  • Akashi H. 1994. Synonymous codon usage in drosophila melanogaster: natural selection and translational accuracy. Genetics. 136:927–935.
  • Bhattacharyya D, Uddin A, Das S, Chakraborty S. 2019. Mutation pressure and natural selection on codon usage in chloroplast genes of two species in pisum l. (Fabaceae: Faboideae). Mitochondrial DNA A DNA Mapp Seq Anal. 30(4):664–673.
  • Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics. 129(3):897–907.
  • Chaney JL, Clark PL. 2015. Roles for synonymous codon usage in protein biogenesis. Annu Rev Biophys. 44:143–166.
  • Chen SL, Lee W, Hottes AK, Shapiro L, Mcadams HH. 2004. Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci USA. 101(10):3480–3485.
  • Chen ZW, Nie HS, Wang YM, Pei HL, Li SS, Zhang LD, Hua JP. 2017. Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes. BMC Genomics. 18:876.
  • Chiapello H, Lisacek F, Caboche M, Henaut A. 1998. Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene. 209(1–-2):GC1–GC38.
  • Drouin G, Daoud H, Xia J. 2008. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Mol Phylogenet Evol. 49(3):827–831.
  • Duret L. 2002. Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev. 12(6):640–649.
  • Duret L, Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci USA. 96(8):4482–4487.
  • Frumkin I, Lajoie MJ, Gregg CJ, Hornung G, Church GM, Pilpel Y. 2018. Codon usage of highly expressed genes affects proteome-wide translation efficiency. Proc Natl Acad Sci USA. 115(21):E4940–E4949.
  • Greenacre MJ. 1993. Correspondence analysis in practice. London: Academic Press.
  • Greenacre M. 2010. Correspondence analysis of raw data. Ecology. 91(4):958–963.
  • Guan DL, Qian ZQ, Ma LB, Bai Y, Xu SQ. 2019. Different mitogenomic codon usage patterns between damselflies and dragonflies and nine complete mitogenomes for odonates. Sci Rep. 9:678.
  • Hershberg R, Petrov DA. 2008. Selection on codon bias. Annu Rev Genet. 42:287–299.
  • Huang M, Zhong Y, Ma X, Hu Q, Fu M, Han Y. 2019. Analysis of codon usage in the mitochondrion genome of Spirodela polyrhiza. Aquat Bot. 156:65–72.
  • Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 2(1):13–34.
  • Ingvarsson PK. 2007. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol Biol Evol. 24(3):836–844.
  • James JE, Piganeau G, Eyre-Walker A. 2016. The rate of adaptive evolution in animal mitochondria. Mol Ecol. 25(1):67–78.
  • Jia W, Higgs PG. 2008. Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol Biol Evol. 25(2):339–351.
  • Jiang Y, Deng F, Wang H, Hu Z. 2008. An extensive analysis on the global codon usage pattern of baculoviruses. Arch Virol. 153(12):2273–2282.
  • Kano A, Andachi Y, Ohama T, Osawa S. 1991. Novel anticodon composition of transfer RNAs in micrococcus luteus, a bacterium with a high genomic G + C content. Correlation with codon usage. J Mol Biol. 221(2):387–401.
  • Kawabe A, Miyashita NT. 2003. Patterns of codon usage bias in three dicot and four monocot plant species. Genes Genet Syst. 78(5):343–352.
  • Liu G, Cao D, Li S, Su A, Geng J, Grover CE, Hu S, Hua J. 2013. The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes. PLoS One. 8(8):e69476.
  • Liu Q, Dou S, Ji Z, Xue Q. 2005. Synonymous codon usage and gene function are strongly related in Oryza sativa. BioSystems. 80(2):123–131.
  • Liu Q, Feng Y, Xue Q. 2004. Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa. Mitochondrion. Mitochondrion. 4(4):313–320.
  • Liu Q, Hu H, Wang H. 2015. Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice (Oryza sativa L.). Mol Genet Genomics. 290(2):649–660.
  • Liu XY, Li Y, Ji KK, Zhu J, Ling P, Zhou T, Fan LY, Xie SQ. 2020. Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis. Genomics. 112(4):2695–2702.
  • Marais G, Duret L. 2001. Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. J Mol Evol. 52(3):275–280.
  • Moriyama EN, Powell JR. 1998. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res. 26(13):3188–3193.
  • Muftuoglu M, Mori MP, Souza-Pinto N. 2014. Formation and repair of oxidative damage in the mitochondrial DNA. Mitochondrion. 17:164–181.
  • Neron B, Menager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C. 2009. Mobyle: a new full web bioinformatics framework. Bioinformatics. 25(22):3005–3011.
  • Osawa S, Ohama T, Yamao F, Muto A, Jukes TH, Ozeki H, Umesono K. 1988. Directional mutation pressure and transfer RNA in choice of the third nucleotide of synonymous two-codon sets. Proc Natl Acad Sci USA. 85(4):1124–1128.
  • Shah K, Cheng Y, Hahn B, Bridges R, Bradbury NA, Mueller DM. 2015. Synonymous codon usage affects the expression of wild type and F508del CFTR. J Mol Biol. 427(6 Pt B):1464–1479.
  • Shang MZ, Liu F, Hua JP, Wang KB. 2011. Analysis on codon usage of chloroplast genome of Gossypium hirsutum. Scientia Agricultura Sinica. 044:245–253.
  • Sharp PM. 1991. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J Mol Evol. 33(1):23–33.
  • Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F. 1988. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res. 16(17):8207–8211.
  • Sharp PM, Li WH. 1986. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol. 24(1–2):28–38.
  • Sharp PM, Li WH. 1987. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol. 4:222–230.
  • Sharp PM, Tuohy TM, Mosurski KR. 1986. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14(13):5125–5143.
  • Shi X, Wang X, Li Z, Zhu Q, Tang W, Ge S, Luo J. 2006. Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias. Gene. 376(2):199–206.
  • Sirihongthong T, Jitobaom K, Phakaratsakul S, Boonarkart C, Suptawiwat O, Auewarakul P. 2019. The relationship of codon usage to the replication strategy of parvoviruses. Arch Virol. 164(10):2479–2491.
  • Smith DR, Hua JM, Lee RW, Keeling PJ. 2012. Relative rates of evolution among the three genetic compartments of the red alga porphyra differ from those of green plants and do not correlate with genome architecture. Mol Phylogenet Evol. 65(1):339–344.
  • Song H, Gao H, Liu J, Tian P, Nan Z. 2017. Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs. Sci Rep. 7(1):14853.
  • Sueoka N. 1995. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol. 40(3):318–325.
  • Sueoka N. 1999. Translation-coupled violation of parity rule 2 in human genes is not the cause of heterogeneity of the DNA G + C content of third codon position. Gene. 238(1):53–58.
  • Tang M, Chen Z, Grover CE, Wang Y, Li S, Liu G, Ma Z, Wendel JF, Hua J. 2015. Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes. BMC Genomics. 16:770.
  • Uddin A, Choudhury MN, Chakraborty S. 2018. Codon usage bias and phylogenetic analysis of mitochondrial Nd1 gene in pisces, aves, and mammals. Mitochondrial DNA A DNA Mapp Seq Anal. 29(1):36–48.
  • Victor MP, Acharya D, Begum T, Ghosh TC. 2019. The optimization of mRNA expression level by its intrinsic properties-insights from codon usage pattern and structural stability of mRNA. Genomics. 111(6):1292–1297.
  • Wang L, Xing H, Yuan Y, Wang X, Saeed M, Tao J, Feng W, Zhang G, Song X, Sun X. 2018. Genome-wide analysis of codon usage bias in four sequenced cotton species. PLoS One. 13(3):e0194372
  • Wei Y, Silke JR, Xia X. 2019. An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria. Sci Rep. 9(1):3184.
  • Wright F. 1990. The ‘effective number of codons’ used in a gene. Gene. 87(1):23–29.
  • Xiao S, Nguyen DT, Wu B, Hao W. 2017. Genetic drift and indel mutation in the evolution of yeast mitochondrial genome size. Genome Biol Evol. 9(11):3088–3099.
  • Yang Q, Yu CH, Zhao F, Dang Y, Wu C, Xie P, Sachs MS, Liu Y. 2019. Erf1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons. Nucleic Acids Res. 47(17):9243–9258.
  • Zhang WJ, Zhou J, Li ZF, Wang L, Gu X, Zhong Y. 2007. Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L. J Integrative Plant Biology. 49(2):246–254.
  • Zhou M, Li X. 2009. Analysis of synonymous codon usage patterns in different plant mitochondrial genomes. Mol Biol Rep. 36(8):2039–2046.