Codon Usage Bias of Chalcone Synthase Gene <i>CHS</i> in Kiwifruit

CHEN Yi-ting; LAI Rui-lian; FENG Xin; GAO Min-xia; ZHANG Chang-he; WU Ru-jian

doi:10.19303/j.issn.1008-0384.2017.011.009

Volume 32 Issue 11

Jan. 2018

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Article Navigation > Fujian Journal of Agricultural Sciences > 2017 > 32(11): 1213-1217

CHEN Yi-ting, LAI Rui-lian, FENG Xin, GAO Min-xia, ZHANG Chang-he, WU Ru-jian. Codon Usage Bias of Chalcone Synthase Gene CHS in Kiwifruit[J]. Fujian Journal of Agricultural Sciences, 2017, 32(11): 1213-1217. doi: 10.19303/j.issn.1008-0384.2017.011.009

Citation:

CHEN Yi-ting, LAI Rui-lian, FENG Xin, GAO Min-xia, ZHANG Chang-he, WU Ru-jian. Codon Usage Bias of Chalcone Synthase Gene CHS in Kiwifruit[J]. Fujian Journal of Agricultural Sciences, 2017, 32(11): 1213-1217. doi: 10.19303/j.issn.1008-0384.2017.011.009

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Codon Usage Bias of Chalcone Synthase Gene CHS in Kiwifruit

doi: 10.19303/j.issn.1008-0384.2017.011.009

1.
Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
2.
Jianning County Bureau of Agriculture, Sanming, Fujian 354500, China

Received Date: 2016-12-27
Rev Recd Date: 2017-06-22
Publish Date: 2017-11-28

Abstract

Abstract

To investage codon usage characteristic of chalcone synthase gene of kiwifruit, CodonW, SPSS, MEGA software and EMBOSS online program were used to analyse codon usgae bias (CUB) of CHS, and phylogenetic tree of CHS between monocotyledon and dicotyledon was constructed in this paper. The results showed that, the effective number of codons (ENc), total GC content (GC) and GC content on the 3^rd site (GC3s) was 57.21, 0.533 and 0.607, respectively. The number of condons, the number of relative synonymous codon usage (RSCU) of which was more than 1.0, was 30, but no codons was with strongly CUB. The cluster tree of CHS based on CUB was closer to the real category system than it did by sequence similarity. According to codon usage frequency, the CUB between CHS of kiwifruit and Arabidopsis thaliana, Escherichia coli were more similar. These results indicated that, the CUB level of CHS was low in kiwifruit, but it was bias toward GC rich codons and synonymous codons with G or C at 3^rd codon position. And CHS in monocotyledons and dicotyledons had the distinctive CUB rules. In addition, Arabidopsis thaliana and Escherichia coli migth be the best receptors for genetic transformation and heterologous expression of CHS in kiwifruit.
- Kiwifruit,
- chalcone synthase,
- codon usage bias,
- cluster analysis

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References(21)

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