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[1]王晓 赵春丽 彭丽云 赖钟雄** 刘生财**.苋菜蓝光受体基因AmCRY1密码子使用模式及分析*[J].应用与环境生物学报,2020,26(01):1-13.[doi:10.19675/j.cnki.1006-687x.2019.04056]
 WANG Xiao,ZHAO Chunli,PENG Liyun,et al.Codon usage patterns and analysis of blue light receptor gene AmCRY1 in Amaranthus tricolor L .*[J].Chinese Journal of Applied & Environmental Biology,2020,26(01):1-13.[doi:10.19675/j.cnki.1006-687x.2019.04056]
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苋菜蓝光受体基因AmCRY1密码子使用模式及分析*()
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
26卷
期数:
2020年01期
页码:
1-13
栏目:
研究论文
出版日期:
2020-01-25

文章信息/Info

Title:
Codon usage patterns and analysis of blue light receptor gene AmCRY1 in Amaranthus tricolor L .*
作者:
王晓 赵春丽 彭丽云 赖钟雄** 刘生财**
福建农林大学园艺植物生物工程研究所 福州 350002
Author(s):
WANG Xiao ZHAO Chunli PENG Liyun LAI Zhongxiong** & LIU Shengcai**
Institute of Horticultural Plant Bioengineering, Fujian Agricultural and Forestry University, Fuzhou 350002, China
关键词:
苋菜AmCRY1基因密码子使用模式
Keywords:
Amaranthus tricolor L . AmCRY1 gene Codon usage patterns
DOI:
10.19675/j.cnki.1006-687x.2019.04056
摘要:
为了解苋菜AmCRY1基因密码子的使用偏好性、与其他物种CRY1基因的同源关系及异源表达受体,利用CodonW与EMBOSS程序及Excel 2017、SPSS 24、Origin 201 8等软件,分析苋菜与其他物种中的CRY1基因的密码子使用特性,比较苋菜AmCRY1基因与模式生物的密码子使用频率。结果表明:苋菜AmCRY1基因的密码子的有效密码子数(ENc)值为54.42,GC含量和GC3含量均低于50%,这表明苋菜AmCRY1偏好使用以A/T结尾的密码子,且在其编码区序列中A+T含量大于G+C;苋菜AmCRY1基因中,偏好性较强的密码子有29个(RSCU > 1),偏好性最强的有1个(RSCU > 2),其中以A/T结尾的密码子有22个,这表明苋菜AmCRY1基因的密码子偏好以A/T结尾,一些氨基酸对密码子的使用具有较强的偏好性;苋菜AmCRY基因的密码子在ENc绘图中的基因位点更接近期望曲线,说明在进化过程中苋菜AmCRY1基因的密码子偏好性受突变压力的影响较大;苋菜AmCRY1基因的密码子使用偏好性参数与石竹目物种相近,同源关系较近物种密码子使用偏好性具有相似性;从密码子使用频率上分析得出,酵母菌表达系统更适合苋菜AmCRY1的异源表达,模式植物拟南芥、烟草、番茄均可作为苋菜AmCRY1基因的遗传转化受体,同苋菜代谢途径相似的甜菜也可以作为苋菜AmCRY1基因的瞬时表达受体。本研究发现苋菜AmCRY1密码子偏好以A/T结尾且受突变压力影响,这可为进一步的功能研究尤其是异源表达验证提供参考。
Abstract:
In order to explore the codon usage bias, homology with CRY1 genes in different species and genetic transformation receptors of amaranth AmCRY1 gene , In this study, CodonW and EMBOSS programs, Excel 2017, SPSS 24, Origin 2018 and other software were used to analyze the codon bias of CRY1 gene in amaranth and other species, and to compare the codon use frequency of AmCRY1 gene and model organisms. Effective number of codons (ENc) of AmCRY1 in amaranth was 54.42, and the content of GC and GC3 were lower than 50%. This indicated that AmCRY1 preferred codons ending with A/T, and the content of A+T in the coding region was higher than that of G+C. Among the codons of amaranth AmCRY1, 29 codons (RSCU > 1) had strong preference, and one codon (RSCU > 2) had the strongest preference. Among them, 22 codons ended with A/T, respectively. This indicated that codons of amaranth AmCRY1 preferred to end with A/T, and some amino acids preferred codon usage. The codon preference of AmCRY1 in amaranth was more affected by mutation pressure in the process of evolution, because the codon loci of AmCRY1 in amaranth were closer to the expected curve in ENC mapping. The codon usage preference parameters of amaranth AmCRY1 gene are similar to those of Caryophylla species, and the codon usage preference of species with similar homology is similar. From the analysis of codon usage frequency, yeast expression system is more suitable for heterologous expression of amaranth AmCRY1. Arabidopsis thaliana, tobacco and tomato can be used as genetic transformation receptors of amaranth AmCRY1. Sugar beet with similar metabolic pathways of amaranth can also be used as transient expression receptors of amaranth AmCRY1. In this study, the codon preference of amaranth AmCRY1 ended with A/T and was affected by mutation pressure, which provided a reference for further functional research, especially for verification of heterologous expression.

相似文献/References:

[1]彭丽云,王云,孙雪丽,等.苋菜AmMYB2基因密码子偏好性与进化分析[J].应用与环境生物学报,2019,25(03):679.[doi:10.19675/j.cnki.1006-687x.201809020]
 PENG Liyun,WANG Yun,SUN Xueli,et al.Codon bias and evolutionary analysis of the AmMYB2 Gene in Amaranthus tricolor L.[J].Chinese Journal of Applied & Environmental Biology,2019,25(01):679.[doi:10.19675/j.cnki.1006-687x.201809020]

备注/Memo

备注/Memo:
收稿日期 Received: 2019-04-28 接受日期 Accepted: 2019-07-03
*福建省自然科学基金项目(2018J01700)和福建农林大学科技创新专项基金项目(CXZX2017174,CXZX2016118,CXZX2017189)资助
**通讯作者 Corresponding author (E-mail: laizx01@163.com; 1215698900@qq.com)
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更新日期/Last Update: 2019-07-05