Analysis of codon usage bias reveals optimal codons in Elaeis guineensis
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Abstract. Aditama R, Tanjung ZA, Sudania WM, Nugroho YA, Utomo C, Liwang T. 2020. Analysis of codon usage bias reveals optimal codons in Elaeis guineensis. Biodiversitas 21: 5331-5337. Codon usage bias of oil palm genome was reported employing several indices, including GC content, relative synonymous codon usage (RSCU), the effective number of codons (ENC), and codon adaptation index (CAI). Unimodal distribution of GC content was observed and matched with non-grass monocots characteristics. Correspondence analysis (COA) on synonymous codon usage bias showed that the main axis was strongly driven by GC content. The ENC and neutrality plot of oil palm genes indicating that natural selection played more vital role compared to mutational bias on shaping codon usage bias. A positive correlation between calculated CAI and experimental data of oil palm gene expression was detected indicating good ability of this index. Finally, eighteen codons were defined as “optimal codons” that may provide a useful reference for heterogeneous expression and genome editing studies.
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References
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Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA. 2010. GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics 11.
Thorrez L, Van Deun K, Tranchevent LC, Lommel LV, Engelen K, Marchal K, Moreau Y, Mechelen I, Schuit F. 2008. Using ribosomal protein as reference: a tale of caution. PLoS ONE 3:3
Wahid MB, Abdullah SNA, Henson IE. 2005. Oil Palm – Achievements and potential. Plant Prod. Sci. 8: 288-297
Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren HE. 2014. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome biol. 15:549
Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics 129: 897-907
Clement Y, Fustier MA, Nabholz B, Glemin S. 2014. The bimodal distribution of genic GC content is ancestral to monocot species. Genome Biol. Evol. 7: 336-348
Corley RHV, Tinker PB. 2015. The Oil Palm. John Wiley & Sons, Chicester.
Figuet E, Ballenghien M, Romiguier J, Galtier N. 2014. Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates. Genome Biol. Evol. 7: 240-250
Frelin L, Ahlen G, Alheim M, Weiland O, Barnfield C, Liljestrom P, Sallberg M. 2004. Codon optimization and mRNA amplification effectively enhances the immunogenicity of the hepatitis C virus nonstructural 3/4A gene. Gene Ther 11: 522-533
Glémin S, Clément Y, David J, Ressayre A. 2014. GC content evolution in coding regions of angiosperm genomes: A unifying hypothesis. Trends Genet. 30: 263-270
Hershberg R, Petrov DA. 2008. Selection on codon bias. Annu. Rev. Genet. 42: 287-299
Ho CL, Tan YC, Yeoh KA, Ghazali AK, Yee WY, Hoh CC. 2016. De novo transcriptome analyses of host-fungal interactions in oil palm (Elaeis guineensis Jacq). BMC Genomics 17:66
Hsiao L, Dangond F, Yoshida T, et al. 2002. A compendium of gene expression in normal human tissues. Phys. Gen. 7: 97-104
Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translation system. J. Mol. Biol. 151: 389-409
Kawabe A, Miyashita NT. 2003. Patterns of codon usage bias in three dicot and four monocot plant species. Genes Genet. Syst.78: 343-352
Ko HJ, Ko SY, Kim YJ, Lee EG, Cho SN, Kang CY. 2005. Optimization of codon usage enchances the immunogenicity of a DNA vaccine encoding mycobacterial antigen AG85B. Infect. Immun. 73(9): 5666-5674
Lei X, Xiao Y, Xia W, Mason AS, Yang Y, Ma Z, Peng M. 2014. RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species. PLos One 9, 1-20
Liu H, He R, Zhang H, Huang Y, Tian M, Zhang J. 2010. Analysis of synonymous codon usage in Zea mays. Mol. Biol. Rep. 37: 677-684
Liu Q. 2006. Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans. BioSystems 85: 99-106
Machado HE, Lawrie DS, Petrov DA. 2017. Strong purifying selection on codon usage bias. bioRxiv 106476. Doi: https://doi.org/10.1101/106476
Marais G, Mouchiroud D, Duret L. 2001. Does recombination improve selection on codon usage? Lesson from nematode and fly complete genomes. Proc. Natl. Acad. Sci 98: 5688-5692
Mazumdar P, Othman RYB, Mebus K, Ramakrishnan N, Harikrishna JA. 2017. Codon usage and codon pair patterns in non-grass monocot genomes. Ann. Bot. 120: 893-909
McInerney JO. 1998. GCUA: General codon usage analysis. Bioinformatics 14: 372-373
Mukhopadhyay P, Basak S, Ghosh TC. 2008. Differential selective constraints shaping codon usage pattern of housekeeping and tissue-specific homologous genes of rice and Arabidopsis. DNA Res. 15: 347-356
Naya H, Rometo H, Carels N, Zavala A, Musto H. 2001. Translational selection shapes codon usage in the GC-rich genome of Chlamydomonas reinhardtii. FEBS Lett. 501: 127-130
Okamoto S, Amaishi Y, Maki I, Enoki T, Mineno J. 2019. Highly efficient genome editing for single-base substitusing using optimized ssODNs with Cas9-RNPs. Sci. Rep. 9, 1-11
Othman NQ, Sulaiman S, Lee YP, Tan JS. 2019. Transcriptomic data of mature oil palm basal trunk tissue infected with Ganoderma boninense. Data in Brief 25: 104288
Peng RH, Yao QH, Xiong AS, Cheng ZM, Li Y. 2006. Codon-modifications and an endoplasmic reticulum-targeting sequence additively enhance expression of an Aspergillus phytase gene in transgenic canola. Plant Cell Rep. 25: 124-132
Puigbò P, Bravo IG, Garcia-Vallve S. 2008. CAIcal: A combined set of tools to assess codon usage adaptaion. Biol. Direct. 3: 1-8
Rouwendal GJA, Mendes O, Wolbert EJH, De Boer AD. 1997. Enhanced expression in tobacco of the gene encoding green fluorescent protein by modification of its codon usage. Plant Mol. Biol. 33: 989-999
Sharp PM, Li WH. 1987. The codon adaptation index – a measure of directional synonymous codon usage bias, and its potential application. Nucl. Ac. Res.15: 1281-1295
Sharp PM, Li WH. 1987. An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 24: 28-38
Shields DC, Sharp PM. 1987. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutation bias. Nucl. Ac. Res. 15: 8023-8040
Singh R, et al. 2013. Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500: 335-339
Spencer, CCA. 2006. Human polymorphism around recombination hotspots. Biochem. Soc. Trans. 34: 535-536
Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA. 2010. GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics 11.
Thorrez L, Van Deun K, Tranchevent LC, Lommel LV, Engelen K, Marchal K, Moreau Y, Mechelen I, Schuit F. 2008. Using ribosomal protein as reference: a tale of caution. PLoS ONE 3:3
Wahid MB, Abdullah SNA, Henson IE. 2005. Oil Palm – Achievements and potential. Plant Prod. Sci. 8: 288-297
Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren HE. 2014. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome biol. 15:549
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