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| Genome-wide analysis of the synonymous codon usage patterns in apple |
| LI Ning*, SUN Mei-hong*, JIANG Ze-sheng, SHU Huai-rui, ZHANG Shi-zhong |
| State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong 271018, P.R.China |
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Abstract Apple (Malus×domestica) has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by CodonW and SPSS (Statistical Product and Service Solutions) programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple.
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Received: 20 March 2015
Accepted:
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| Fund: This work was supported by the National Natural Science Foundation of China (31401822). |
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Corresponding Authors:
ZHANG Shi-zhong, Tel: +86-538-8242364, E-mail: shizhong@sdau.edu.cn; SHU Huai-rui, Tel: +86-538-8242364, E-mail: hrshu@sdau.edu.cn
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| About author: * These authors contributed equally to this study. |
Cite this article:
LI Ning, SUN Mei-hong, JIANG Ze-sheng, SHU Huai-rui, ZHANG Shi-zhong.
2016.
Genome-wide analysis of the synonymous codon usage patterns in apple. Journal of Integrative Agriculture, 15(05): 983-991.
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