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 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(03):679-686.[doi:10.19675/j.cnki.1006-687x.201809020]





Codon bias and evolutionary analysis of the AmMYB2 Gene in Amaranthus tricolor L.
福建农林大学,园艺植物生物工程研究所 福州 350002
PENG Liyun1 WANG Yun1 SUN Xueli1 ZHAO Chunli1 WANG Xiao1 LAI Zhongxiong1** & LIU Shengcai1**
Institute of Horticultural Plant Biological Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Amaranthus tricolor L AmMYB2 gene codon usage bias evolution analysis
S668.1: Q78
为了解苋菜AmMYB2基因的密码子使用偏好性、与不同物种中调控色素相关的R2R3-MYB基因的同源关系及异源表达受体,利用Codon W与EMBOSS程序及Excel、SPSS 、Origin等软件,分析苋菜与其他物种中调控色素代谢的R2R3-MYB基因的密码子使用偏好性,比较苋菜AmMYB2基因与模式生物的密码子使用频率. 结果显示:苋菜AmMYB2基因中,所有密码子的GC、GC1、GC2、GC3含量均低于50%,偏好性较强的密码子有17个(RSCU > 1),偏好性最强的有7个(RSCU > 2),其中以A/T结尾的密码子有19个,表明苋菜AmMYB2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AmMYB2基因密码子的有效密码子数(Effective number of codons,ENC)值为49.63,苋菜AmMYB2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AmMYB2基因的密码子偏好性受突变压力的影响较大;苋菜基因与甜菜色素代谢相关的R2R3-MYB基因的密码子使用偏好性参数相近,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AmMYB2基因的异源表达,模式植物拟南芥、烟草、番茄均可作为苋菜AmMYB2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AmMYB2基因的瞬时表达受体. 本研究可为苋菜AmMYB2基因功能的进一步研究提供重要参考. (图5 表2 参31)
This study was done to explore the codon usage bias, homology with the R2R3-MYB genes associated with pigment regulation in various species, and genetic transformation receptors of the AmMYB2 gene of amaranth (Amaranthus tricolor L.). The Codon W and EMBOSS online programs and Excel, SPSS, and Origin software were used to analyze the codon usage bias of the amaranth AmMYB2 gene. Correlation analysis was conducted to compare the codon usage bias of the amaranth AmMYB2 gene and the R2R3-MYB genes controlling pigment metabolism in other species with those in model organisms for which relatively mature genetic transformation systems are available. The?results showed that the content of GC, GC1, GC2, and GC3 in the amaranth AmMYB2 gene are all lower than 50%. There are seventeen more strongly favored codons (RSCU > 1) in this gene, seven of which were aggressively favored over others (RSCU > 2). Among these, there are 19 codons ending in A or T, which showed that the genetic codon bias in the amaranth AmMYB2 gene favors codons with A or T as the third bit in the codon, and thus favors the use these highly favored codons in some amino acids. The effective number of codons (ENC) in the amaranth AmMYB2 gene was 49.63, and the locus of the amaranth AmMYB2 gene in the ENC plot was closer to the desired curve, which showed that the codon bias of the amaranth AmMYB2 gene has mainly been affected by mutation pressure. The codons of the R2R3-MYB gene related to the metabolism of beet pigment were similar in their preference parameters to amaranth, and the codon bias parameters of the amaranth AmMYB2 gene were also similar to those of the R2R3-MYB genes of closely related species. Based on the analysis of the frequency of codon usage across species, a yeast expression system was found to be the most suitable for use with the AmMYB2 gene, and the model plants Arabidopsis, tobacco, and tomato could be used as genetic transformation receptors of the AmMYB2 gene. Because of the similarity of its metabolic pathways to those of amaranth, beet can also act as the transient expression receptor of the amaranth AmMYB2 gene. This study provides important reference information for further studies on the function of the AmMYB2 gene in amaranth.


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更新日期/Last Update: 2019-06-25