蕙兰一个PEBP家族基因的克隆及生物信息学分析  

Cloning and bioinformatics analysis of a PEBP family gene from Cymbidium faberi

作　　者：楚志刚 田云芳 CHU Zhigang;TIAN Yunfang(College of Information Science and Technology,Zhengzhou Normal University,Zhengzhou 450044,China;College of Life Sciences,Zhengzhou Normal University,Zhengzhou 450044,China;Zhengzhou Key Laboratory of Ornamental and Medicinal Resources Plants,Zhengzhou 450044,China)

机构地区：[1]郑州师范学院信息科学与技术学院,河南郑州450044 [2]郑州师范学院生命科学学院,河南郑州450044 [3]郑州市观赏药用特色资源植物重点实验室,河南郑州450044

出　　处：《浙江农业学报》2022年第8期1679-1691,共13页Acta Agriculturae Zhejiangensis

基　　金：河南省科技攻关计划(212102110184);河南省高等学校重点科研项目(22A210026);河南省高等学校青年骨干教师培养计划(2018GGJS162)。

摘　　要：为了初步探究蕙兰磷脂酰乙醇胺结合蛋白(phosphatidyl ethanolamine-binding proteins,PEBP)基因的特征与功能,以蕙兰花蕾期叶片为材料,利用反转录PCR(RT-PCR)结合cDNA末端快速扩增(RACE)技术克隆基因,使用在线生物信息学工具进行蛋白结构与功能预测,通过R语言和3个在线软件(CodonW、CHIPS和CUSP)分析该基因的密码子偏好性。结果表明,克隆得到的蕙兰PEBP基因包含531 bp长度的开放阅读框(ORF),对应编码氨基酸176个。该基因命名为CfPEBP(登录号MT795710)。生物信息学分析表明,CfPEBP分子式为C_(882)H_(1366)N_(254)O_(260)S_(5),分子量为19848.39 u;等电点为6.42;具有15个磷酸化位点。CfPEBP蛋白无信号肽结构域,具有PEBP功能域。进化树分析结果表明,CfPEBP蛋白与春兰FT进化距离最近,同源性为100%。分析显示,CfPEBP的密码子偏好性表现较弱;依据同义密码子相对使用度(RSCU)分析较强偏性密码子有GGC、AGA、AGU、AAG、CCA、CUC(RSCU≥2.00)。18个物种PEBP基因RSCU值分析表明,蕙兰HQ164434、文心兰KJ909968、文心兰EU583502、石斛MF063061、香蕉KF853468、牵牛AB154823的密码偏好性较强,均有25个以上RSCU值>1.00的密码子。PEBP家族基因对于GGC、AGG、AGA、AGC、AGU、UGC、GAG、AAG、UAC、GCC、CCA、CUC的偏好性超过其他密码子。CfPEBP基因在蕙兰盛花期叶中相对表达量最高,花蕾期花蕾和盛花期花葶中表达量次之,其他组织几乎不表达。本研究为蕙兰PEBP家族基因功能的进一步研究提供了基础。In order to explore the characteristics and function of PEBP gene family in Cymbidium faberi,the gene was cloned by reverse transcription-polymerase chain reaction(RT-PCR)combined with rapid-amplification of cDNA ends(RACE).R language,CodonW,CHIPS and CUSP software were used to analyze the codon preference,and the protein structure and function of the gene were predicted by using bioinformatics tools.The results showed that the cDNA sequence of PEBP gene contained 531 bp open reading frame(ORF)and encoded 176 amino acids.The gene was named as CfPEBP(Accession No.MT795710).The molecular formula of CfPEBP was C_(882)H_(1366)N_(254)O_(260)S_(5) with molecular weight of 19848.39 u,pI of 6.42,and phosphorylation sites of 15.CfPEBP protein has no signal peptide domain and has PEBP functional domain.Phylogenetic tree analysis showed that CfPEBP protein had the closest evolutionary distance with FT gene of Cymbidium goeringii,and the homology was 100%.Codon preference analysis showed that the codon preference of CfPEBP was not obvious;based on the relative synonymous codon usage(RSCU)value,GGC,AGA,AGU,AAG,CCA,CUC(RSCU≥2)were the most preferred codons.The RSCU value analysis of PEBP gene in 18 species showed that there were more than 25 codons with RSCU value>1 in Cymbidium faberi,Oncidium hybrid(KJ909968),Oncidium hybrid(EU583502),Dendrobium hybrid(MF063061),Musa acuminata(KF853468)and Ipomoea nil(AB154823).PEBP family genes had more preference than other codons for GGC,AGG,AGA,AGC,AGU,UGC,GAG,AAG,UAC,GCC,CCA,CUC.The relative expression level of CfPEBP gene was the highest in the leaves of Cymbidium faberi at flowering stage,followed by flower bud at bud stage and inflorescence rachis at full-blossom stage.This study provided the basis for further study on the function of CfPEBP gene.

关 键 词：蕙兰 PEBP 生物信息学分析 密码子偏好性 表达 

分 类 号：S682.31[农业科学—观赏园艺]