辣椒和番茄PIF基因家族密码子偏好性分析  

Codon Bias Analysis of PIF Gene Family in Pepper and Tomato

作　　者：陈悦 仇学文 李钰 陈金印[1] 杨有新[1] 余婷 Chen Yue;Qiu Xuewen;Li Yu;Chen Jinyin;Yang Youxin;Yu Ting(Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits&Vegetables,Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables,College of Agronomy,Jiangxi Agricultural University,Nanchang,330045)

机构地区：[1]江西农业大学农学院,江西省果蔬采后处理关键技术与质量安全协同创新中心,江西省果蔬保鲜与无损检测重点实验室,南昌330045

出　　处：《分子植物育种》2023年第17期5602-5610,共9页Molecular Plant Breeding

基　　金：江西省主要学科学术和技术带头人培养计划青年人才项目(20204BCJL23044);江西省现代农业产业技术体系建设专项(JXARS-06)共同资助。

摘　　要：本研究选取辣椒和番茄两种茄科作物的光敏色素互作因子(phytochrome-interacting factors,PIF)基因家族为研究对象,利用CodonW和CUSP等软件,分析这两种作物PIF基因家族的密码子偏好性。结果发现:辣椒和番茄PIF基因家族的密码子偏好性都较弱,大多数PIF基因家族成员都偏好以A或T(U)结尾,而CaPIF8和SlPIF8a偏好以C结尾;在辣椒中鉴定出30个高频密码子,番茄中鉴定出27个高频密码子,两者的高频密码子均偏好以A或T(U)结尾,其中偏性最强的密码子均为AGA;两者PIF基因家族密码子同义密码子第3位碱基GC含量(GC3s)均与有效密码子数(ENC)呈显著相关性;RSCU聚类分析结果也与CDS聚类结果基本一致;从ENC-plot、偏倚分析(PR2-plot)、中性绘图可以判断碱基突变与自然选择均会影响密码子使用,但自然选择的影响更大。本研究为日后辣椒和番茄的PIF基因家族功能验证提供一定的理论依据。Phytochrome-interacting factors(PIF) gene families in two Solanaceae crops,pepper and tomato,were selected as codon bias analysis in this study.CodonW and CUSP were used to analyze PIF gene family codon preference in these two Solanaceae crops.The results showed that the preferences of PIF gene family of the pepper and tomato were weak.Most members of the PIF gene family preferred to end with A or T(U),while CaPIF8 and SlPIF8a preferred to end with C.30 high frequency codons were identified in pepper and 27 were identified in tomato.Both of the high frequency codons preferred to end with A or T(U),and AGA was the most biased codon.The content of the third base GC(GC3s) of the codon synonymous codon of the PIF gene family was significantly correlated with the effective codon number(ENC) both of pepper and tomato.RSCU cluster analysis are basically consistent with CDS cluster analysis.From ENC-plot,bias analysis(PR2-plot) and neutral plot,it can be concluded that both base mutation and natural selection affect codon use,but the influence of natural selection is greater.This study provided some theoretical assistance for functional verification of pepper and tomato PIF gene family in the future.

关 键 词：番茄 辣椒 PIF基因家族 密码子偏好性 

分 类 号：S641.2[农业科学—蔬菜学] S641.3[农业科学—园艺学]