红蓝光对草莓转录组特异表达基因密码子使用偏好性的影响

doi:10.3969/j.issn.1004-1524.2017.04.08

浙江农业学报 ›› 2017, Vol. 29 ›› Issue (4): 566-574.DOI: 10.3969/j.issn.1004-1524.2017.04.08

红蓝光对草莓转录组特异表达基因密码子使用偏好性的影响

冯琛, 汤浩茹^*, 江雷雨, 宋霞, 张云婷, 叶云天, 陈清, 孙勃

四川农业大学园艺学院, 四川成都 611130

收稿日期:2016-12-06 出版日期:2017-04-20 发布日期:2017-04-27
通讯作者: 汤浩茹,E-mail:htang@sicau.edu.cn
作者简介:冯琛(1992—),男,河北邢台人,硕士研究生,主要从事分子生物学在果树上的应用研究。E-mail:fengchensicau@163.com

Analysis of codon usage bias of specific genes in strawberry transcriptome under the red and blue light

FENG Chen, TANG Haoru^*, JIANG Leiyu, SONG Xia, ZHANG Yunting, YE Yuntian, CHEN Qing, SUN Bo

College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China

Received:2016-12-06 Online:2017-04-20 Published:2017-04-27

摘要/Abstract

摘要： 草莓转录组中特异表达基因密码子的使用偏好性分析能够为基因异源表达提供参考。为了探究红蓝光处理对草莓转录组特异表达基因密码子使用偏好性的影响,以四川农业大学果树分子生物学实验室前期红蓝光处理后的草莓转录组数据为原始实验数据,以白光处理的草莓转录组数据为原始对照数据,利用perl语言及测序结果中的FPKM值(fragments per kb per million fragments)对转录组数据进行筛选,通过Mobyle在线程序对筛选得到的特异表达基因进行密码子偏好性分析。结果表明:蓝光处理后的特异表达基因有114条,大约是红光处理的2倍;从GC含量结合GC3s含量来看,红光和蓝光处理中的特异表达基因各自均有91%偏好使用以A/T结尾的密码子;最优密码子中,红光特异基因偏好以A/T结尾的最优密码子所占的比例比蓝光特异基因多2.84%;密码子使用频率比较结果发现,酵母表达系统更适合用于2种处理特异表达基因的异源表达实验,拟南芥更适合作为2种处理特异表达基因的转基因受体。

关键词: 红蓝光, 转录组, 草莓, 密码子偏好性

Abstract: Analysis of codon usage bias of specific genes in strawberry transcriptome could provide reference for heterologous expression of genes. To understand the influence of red and blue light on codon usage bias, the original experimental data, which was transcriptome of strawberry treated with red and blue light, and the original control data, which was transcriptome of strawberry treated with white light, were screened by perl language and FPKM (fragments per kb per million fragments) value, then, Mobyle online program were used to analyze the codon usage bias of it. The results showed that there were 114 specific genes under the blue light, twice as that under the red light; From the point of view of GC content combined with GC3s (GC content of the third position), 91 percent of specific genes under red and blue light, respectively, were bias toward the synonymous codons with A and T at the third codon position; In addition, the fraction of specific genes under the red light between optimal codons with A and T at the third codon position and optimal codons was 2.84 percent more than that under the blue light. According to codon usage frequency, the Pichia pastoris expression system was more suitable for heterologous expression of specific genes of the two treatments, Arabidopsis thaliana might be the best receptor for transgenosis.

Key words: red and blue light, transcriptome, strawberry, codon usage bias

中图分类号:

S432.4⁺1

冯琛, 汤浩茹, 江雷雨, 宋霞, 张云婷, 叶云天, 陈清, 孙勃. 红蓝光对草莓转录组特异表达基因密码子使用偏好性的影响[J]. 浙江农业学报, 2017, 29(4): 566-574.

FENG Chen, TANG Haoru, JIANG Leiyu, SONG Xia, ZHANG Yunting, YE Yuntian, CHEN Qing, SUN Bo. Analysis of codon usage bias of specific genes in strawberry transcriptome under the red and blue light[J]. , 2017, 29(4): 566-574.

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红蓝光对草莓转录组特异表达基因密码子使用偏好性的影响

Analysis of codon usage bias of specific genes in strawberry transcriptome under the red and blue light

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