|
|
|
|
|
| Comparative analysis of flower-meristem-identity gene APETALA2 (AP2) codon in different plant species |
| WU Yan-qing1, 2, LI Zhi-yuan2, ZHAO Da-qiu2, TAO Jun1, 2 |
1 College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P.R.China
2 Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, P.R.China |
|
|
|
|
Abstract The flower-meristem-identity gene APETALA2 (AP2), one of class-A genes, is involved in the establishment of the floral meristem and the forming of sepals and petals. Codon usage bias (CUB) identifies differences among species, meanwhile dynamic analysis of base composition can identify the molecular mechanisms and evolutionary relationships of a specific gene. In this study, eight coding sequences (CDS) of AP2 gene were selected from different plant species using the GenBank database. Their nucleotide composition (GC content), genetic index, relative synonymous codon usage (RSCU) and relative codon usage bias (RCUB) were calculated with R Software to compare codon bias and base composition dynamics of AP2 gene codon usage patterns in different plant species. The results showed that the usage of AP2 gene codons from different plant species were influened by GC bias, especially GC3s. Overall, base composition analysis indicated that the usage frequency of codon AT in the gene coding sequence was higher than GC among AP2 gene CDS from different plant species. Furthermore, most AP2 gene CDSs ended with AT; AGA, GCU and UGU had relatively high RSCU values as the most dominant codon; the usage characteristic of the AP2 gene codon in Malus domestica was similar to that of Vitis vinifera; Paeonia lactiflora was similar to Paeonia suffruticosa and Solanum lycopersicum was similar to Petunia×hybrida. There was a moderate preference in the usage of AP2 gene codon among different plant species from relatively low frequency of optimal codon (Fop) values and high effective number of codons (ENC) value. This study has revealed the usage characteristics of the AP2 gene codon from the comparision of AP2 gene codon preference and base dynamics in different plant species and provide a platform for further study towards transgenic engineering and codon optimization.
|
|
Received: 06 March 2017
Accepted:
|
| Fund: This study was supported by the National Natural Science Foundation of China (31372097), and the Agricultural Science&Technology Independent Innovation Fund of Jiangsu Province, China (CX(13)2014). |
|
Corresponding Authors:
Correspondence TAO Jun, Tel: +86-514-87997219, Fax: +86-514-87347537, E-mail: taojun@yzu.edu.cn
|
| About author: WU Yan-qing, E-mail: yqwu19880928@126.com; |
Cite this article:
WU Yan-qing, LI Zhi-yuan, ZHAO Da-qiu, TAO Jun.
2018.
Comparative analysis of flower-meristem-identity gene APETALA2 (AP2) codon in different plant species. Journal of Integrative Agriculture, 17(04): 867-877.
|
| Akashi H. 1995. Inferring weak selection from patterns of polymorphism and divergence at “silent” sites in Drosophila DNA. Genetics, 139, 1067–1076.Angellotti M C, Bhuiyan S B, Chen G, Wan X F. 2007. CodonO: Codon usage bias analysis within and across genomes. Nucleic Acids Research, 35, 132–136.Bragg J G, Quigg A, Raven J A, Wagner A. 2012. Protein elemental sparing and codon usage bias are correlated among bacteria. Molecular Ecology, 21, 2480–2487.Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics, 129, 897–907.Butt A M, Nasrullah I, Tong Y. 2014. Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PLoS ONE, 9, e90905.Carbone A, Zinovyev A, Kepes F. 2003. Codon adaptation index as a measure of dominating codon bias. Bioinformatics, 19, 2005–2015.Chiapello H, Lisacek F, Caboche M, Hénaut A. 1998. Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene, 209, GC1–GC38.Das S, Sandip P, Chitra D. 2006. Synonymous codon usage in adenoviruses: Influence of mutation, selection and protein hydropathy. Virus Research, 117, 227–236.Duret L. 2000. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends in Genetics, 16, 287–289.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. Fox J M, Erill I. 2010. Relative codon adaptation: A generic codon bias index for prediction of gene expression. DNA Research, 17, 185–196.Fuglsang A. 2004. The ‘effective number of codons’ revisited. Biochemical and Biophysical Research Communications, 317, 957–964.Ge J T, Zhao D Q, Han C X, Wang J, Hao Z J, Tao J. 2014. Cloning and expression of floral organ development-related genes in herbaceous peony (Paeonia lactiflora Pall.). Molecular Biology Reports, 41, 6493–6503.Gouy M, Gautier C. 1982. Codon usage in bacteria: Correlation with gene expressivity. Nucleic Acids Research, 10, 7055–7074.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, r43–r74.Gustafsson C, Govindarajan S, Minshull J. 2004. Codon bias and heterologous protein expression. Trends in Biotechnology, 22, 346–353.Hassan S, Mahalingam V, Kumar V. 2009. Synonymous codon usage analysis of thirty two mycobacteriophage genomes. Advances in Bioinformatics, 316936.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 translational system. Journal of Molecular Biology, 151, 389–409.Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution, 2, 13–34.Jia R Y, Cheng A C, Wang M S, Xin H Y, Guo Y F, Zhu D K, Qi X F, Zhao L C, Ge H, Chen X Y. 2009. Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus. Virus Genes, 38, 96–103.Jofuku K D, Boer B G, Van Montagu M, Okamuro J K. 1994. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. The Plant Cell, 6, 1211–1225.Karlin S, Mrazek J. 1996. What drives codon choices in human genes. Journal of Molecular Biology, 262, 459–472.Lavner Y, Kotlar D. 2005. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene, 345, 127–138.Li C, Pan L L, Wang Y, Wang J, Ding Z T. 2014. Codon bias of the gene for chloroplast glycerol-3-phosphate acyltransferase in Camellia sinensis (L.) O. Kuntze. Biochemical Systematics and Ecology, 55, 212–218.Li W H. 1987. Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. Journal of Molecular Evolution, 24, 337–345.Lithwick G, Margalit H. 2005. Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Research, 33, 1051–1057.Liu H, He R, Zhang H, Huang Y, Tian M, Zhang J. 2010. Analysis of synonymous codon usage in Zea mays. Molecular Biology Reports, 37, 677–684.Liu Q P, Feng Y, Zhao X A, Dong H, Xue Q Z. 2004. Synonymous codon usage bias in Oryza sativa. Plant Science, 167, 101–105.Liu Q P, Hu H C, 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.). Molecular Genetics and Genomics, 290, 649–660.Maes T, Van de Steene N, Zethof J, Karimi M, D’Hauw M, Mares G, Van Montagu M, Gerats T. 2001. Petunia AP2-like genes and their role in flower and seed development. The Plant Cell, 13, 229–244.Mandlik V, Shinde S, Singh S. 2014. Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation. BMC Evolutionary Biology, 14, 142.Mcinerney J O. 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.Morton B R, Wright S I. 2007. Selective constraints on codon usage of nuclear genes from Arabidopsis thaliana. Molecular Biology and Evolution, 24, 122–129.Muhammad Y K B, Abdul G K, Muhammad D. 2012. The relationship between codon usage bias and salt resistant genes in Arabidopsis thaliana and Oryza sativa. Pure Applied Biology, 1, 48–51.Palidwor G A, Perkins T J, Xia X. 2010. A general model of codon bias due to GC mutational bias. PLoS ONE, 5, e13431.Pan L L, Wang Y, Hu J H, Ding Z T, Li C. 2013. Analysis of codon use features of stearoyl-acyl carrier protein desaturase gene in Camellia sinensis. Journal of Theoretical Biology, 334, 80–86.Peden J F. 1999. Analysis of codon usage. Ph D thesis, University of Nottingham, UK.Ren L. 2011. Cloning and expression of floral organ development related genes in tree peony. Ph D thesis, Chinese Academy of Foresty. (in Chinese)Rice P, Longden I, Bleasby A. 2000. EMBOSS: The European molecular biology open software suite. Trends in Genetics, 16, 276–277.Romero H, Musto H, Zavala A. 2000. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Research, 28, 2084–2090.Roymondal U, Das S, Sahoo S. 2009. Predicting gene expression level from relative codon usage bias: An application to Escherichia coli genome. DNA Research, 16, 13–30.Sharp P M, Bailes E, Grocock R J, Peden J F, Sockett R E. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Research, 33, 1141–1153.Sharp P M, Li W H. 1986. An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution, 24, 28–38.Shi S L, Jiang Y R, Liu Y Q, Xia R X, Qin L. 2013. Selective pressure dominates the synonymous codon usage in Parvoviridae. Virus Genes, 46, 10–19.Shields D C, Sharp P M, Higgins D G, Wright F. 1988. “Silent” sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons. Molecular Biology and Evolution, 5, 704–716.Song C N, Fang J G, Wang C, Shangguan L F, Zhang Z. 2009. Cloning and expression analysis of APETLA2 gene from Poncirus trifoliata based on EST database. Acta Horticulturae Sinica, 36, 799–806. (in Chinese)Song H, Wang P F, Ma D C, Xia H, Zhao C Z, Zhang Y, Zhao S Z. 2015. Analysis of codon usage bias of WRKY transcription factors in Medicago truncatula. Journal of Agricultural Biotechnology, 23, 203–212. (in Chinese)Stenico M, Lloyd A T, Sharp P M. 1994. Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational biases. Nucleic Acids Research, 22, 2437–2446.Su H Y, Zhou S M, Wang L, Zhang X S, Shu H R. 2005. Cloning and expression analysis of APETALA2 homologous genes in strawberry. Acta Botanica Boreali-occidentalia Sinica, 25, 1937–1942. (in Chinese)Supek F, Vlahovicek K. 2005. Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. BMC Bioinformatics, 6, 182.Tao P, Dai L, Luo M C, Tang F Q, Tien P, Pan Z S. 2009. Analysis of synonymous codon usage in classical swine fever virus. Virus Genes, 38, 104–112.Tatarinova T V, Alexandrov N N, Bouck J B, Feldmann K A. 2010. GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics, 11, 308.Urrutia A O, Hurst L D. 2003. The signature of selection mediated by expression on human genes. Genome Research, 13, 2260–2264.Vicario S, Moriyama E N, Powell J R. 2007. Codon usage in twelve species of Drosophila. BMC Evolutionary Biology, 7, 226–226.Wong G K S, Wang J, Tao L, Tan J, Zhang J G, Douglas A P, Yu J. 2002. Compositional gradients in Gramineae genes. Genome Research, 12, 851–856.Wright F. 1990. The ‘effective number of codons’ used in a gene. Gene, 87, 23–29.Wu Y Q, Zhao D Q, Tao J. 2015. Analysis of codon usage patterns in Herbaceous Peony (Paeonia lactiflora Pall.) based on transcriptome data. Genes, 6, 1125–1139.Xu C, Cai X, Chen Q, Zhou H, Cai Y, Ben A. 2011. Factors affecting synonymous codon usage bias in chloroplast genome of Oncidium gower ramsey. Evolutionary Bioinformatics, 7, 271–278.Xu C, Cai X N, Qian B L, Ben A L. 2012. Codon usage bias in Vitis vinifera. Acta Botanica Boreali-Occidentalia Sinica, 32, 409–415. (in Chinese)Yang Z, Nielsen R. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Molecular Biology and Evolution, 25, 568–579.Zeng Y, Hu J Y, Li Z J. 2001. MADS-box genes in the evolution of flower development. Plant Physiology Communications, 37, 281–287. (in Chinese) |
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
