XIE Xueguo,ZHANG Zhongrong,LYU Hui,et al.Analysis of Genetic Codon Usage Preference in Pepper PPO Gene Family[J].Northern Horticulture,2022,(07):1-7.[doi:10.11937/bfyy.20213870]
辣椒PPO基因家族密码子偏好性分析
- Title:
- Analysis of Genetic Codon Usage Preference in Pepper PPO Gene Family
- Keywords:
- pepper; PPO gene family; codon preference; correlation analysis
- 文献标志码:
- A
- 摘要:
- 以辣椒多酚氧化酶家族（PPOs）为研究对象，利用CUSP、CHIPS及CodonW 1.4.4 等软件对辣椒PPO基因9个密码子进行分析，研究了辣椒PPOs密码子偏好性特征，以期为辣椒PPO基因家族密码使用模式和分子进化及功能提供参考依据。结果表明：辣椒PPO家族基因偏好性较弱，偏好以A或U（T）结尾的密码子，其中存在28个高频密码子（RSCU>1），4个偏好性较强密码子（RSCU>1.6）和1个偏好性最强密码子（RSCU>2）。聚类结果显示，基于CDS序列聚类效果更好；CaPPO1单独聚为一类，其余8个基因较为接近。相关性分析表明PPO家族基因密码子的偏好性主要影响因素是密码子第3位碱基GC含量(GC3s)。此外，GC、C3s也存在一定的影响。ENC图、中性绘图结果表明自然选择对PPO家族基因密码子偏好性的影响更大。
- Abstract:
- Taking the pepper polyphenol oxidase family (PPOs) as the research object,the 9 codons of pepper PPO gene were analyzed by software such as CUSP,CHIPS and CodonW 1.4.4,and the codon preference characteristics of pepper PPO gene were studied，in order to provide reference for the use pattern,molecular evolution and functional exploration of the PPO gene code of pepper.The results showed that pepper PPO family genes had weak preference for codons ending in A or U (T),including 28 high-frequency codons (RSCU>1),4 strong preference codons (RSCU>1.6) and one strong preference codon (RSCU>2).The clustering results showed that the clustering effect based on CDS sequence was better;CaPPO1 was clustered into one group,and the other 8 genes were close. Correlation analysis showed that the main influencing factor of codon preference of PPO family genes was the GC content of codon 3 base (GC3s).In addition,GC and C3s also have some effects.The results of ENC and neutral mapping showed that natural selection had a greater impact on the codon preference of PPO family genes.
参考文献/References:
[1]CAIL I L,DONG Q L,JING L,et al.Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza[J].Scientific Reports,2017,7(1):44622.[2]MAYER A M.Polyphenol oxidases in plants and fungi:Going places? A review[J].Phytochemistry,2006,67(21):2318-2331.[3]THIPYAPONG P,HUNT M D,STEFFENS J C.Antisense downregulation of polyphenol oxidase results in enhanced disease susceptibility[J].Planta,2004,220(1):105-117.[4]SHANFA L,CHENMIN Y,VINCENT C L.Conservation and diversity of microRNA-associated copper-regulat ory networks in Populus trichocarpa[J].Journal of Integr Plant Biol,2011，53(11):879-891.[5]LI L,STEFFENS C J.Overexpression of polyphenol oxidase in transgenic tomato plants results in enhanced bacterial disease resistance[J].Planta,2002;215(2):239-247.[6]RICHTER C,DIRKS M E,GRONOVER C S,et al.Silencing and heterologous expression of ppo-2 indicate a specific function of a single polyphenol oxidase isoform in resistance of dandelion (Taraxacum officinale) against Pseudomonas syringae pv.tomato[J].Molecular Plant-microbe Interactions,2012（25）：200-210.[7]FUERST E P,OKUBARA P A,ANDERSON J V,et al.Polyphenol oxidase as a biochemical seed defense echanism[J].Frontiers in Plant Science,2014（5）:689.[8]LIU H,HE R,ZHANG H,et al.Analysis of synonymous codon usage in Zea mays[J].Molecular Biology Reports,2010,37(2):677-684.[9]CHIAPELLO H,LISACEK F,CABOCHE M,et al.Codon usage and gene function are related in sequences of Arabidopsis thaliana[J].Gene,1998,209:1-38.[10]LIU Q P,FENG Y,ZHAO X A,et al.Synonymous codon usage bias in Oryza sativa[J].Plant Science,2004(167):101-105.[11]BRAGG J G,QUIGG A,RAVEN J A,et al.Protein elemental sparing and codon usage bias are correlated among bacteria[J].Molecular Ecology,2012（21）:2480-2487.[12]MEGANATHAN P R,PAGAN H J T,MCCULLOCH E S,et al.Complete mitochondrial genome sequencesof three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to abasal split in Chiroptera[J].Gene,2012,492:121-129.[13]NIE X,DENG P,FENG K,et al.Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family[J].Plant Molecular Biology Reporter,2014（32）：828-840.[14]PARAN I,KNAAP E V D.Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper[J].Journal of Experimental Botany,2007,58(14):3841-3852.[15]QIN C,YU C,SHEN Y,et al.Whole-genome sequencing of cultivated and wild peppers provides insights int Capsicum domestication and specialization[J].Proceedings of the National Academy of Sciences,2014,111(14):5135-5140.[16]ZHANG J,LI B,YANG Y,et al.Genome-wide characterization and expression profiles of the superoxide dismutase gene family in Gossypium[J].International Journal of Genomics,2016(6):1-11.[17]宗秋芳,黄焱杰,吴丽思,等.猪Claudin家族基因密码子使用偏好性分析[J].浙江农业学报,2018,30(12):2007-2017.[18]WRIGHT F.The ‘effective number of codons’ used in a gene[J].Gene,1990,87(1):23-29.[19]STENICO M,LLOYD A T,SHARP P M.Codon usage in Caenorhabditis elegans:Delineation of translational selection and mutational biases[J].Nucleic Acids Research,1994,22(13):2437-2446.[20]时慧，王玉，杨路成，等.茶树抗寒调控转录因子ICE1密码子偏性分析[J].园艺学报,2012,39(7):1341-1352.[21]SUEOKA N.Directional mutation pressure and neutral molecular evolution[J].Proceedings of the National Academy of Sciences,1988，85(8):2653-2657.[22]赵森,邓力华,陈芬.不同植物FERONIA基因密码子使用偏好性分析[J].江苏农业学报,2020,36(5):1073-1081.[23]李媛,多杰措,熊辉岩,等.大麦HD-Zip基因家族密码子偏好性分析[J].麦类作物学报,2020,40(2):144-153.[24]惠小涵,程婷婷,柯卫东,等.莲藕PPO基因密码子偏好性特征分析[J].江苏农业学报,2020,36(2):438-446.[25]宋辉,王鹏飞,马登超,等.蒺藜苜蓿 WRKY转录因子密码子使用偏好性分析[J].农业生物技术学报,2015,23(2):207.[26]简雪艳,杨菊.木通叶绿体基因组密码子偏好性分析[J].分子植物育种,2021,36(2):1-12.[27]段淋渊,戴国礼,焦恩宁,等.枸杞自交不亲和基因S-RNase密码子偏性分析[J].西南林业大学学报(自然科学版),2020,40(2):44-52.[28]赵春丽,彭丽云,王晓,等.苋菜AtGAI基因密码子偏好性与进化分析[J].中国农业大学学报,2019,24(12):10-22.[29]郭秀丽,王玉,杨路成,等.茶树〖STBX〗CBF1〖STBZ〗基因密码子使用特性分析[J].遗传,2012,34(12):1614-1623.[30]聂江婷.籽粒苋PEPC、PPDK启动子功能研究和PPDK基因密码子分析[D].大同：山西大学,2015.
相似文献/References:
[1]胡凤霞,唐艳领,刘金,等.辣椒砧木的筛选及其耐盐性研究[J].北方园艺,2013,37(04):24.
[2]陈 潇,盛萍萍,刘润进,等.西瓜与辣椒间作体系接种AM真菌对连作西瓜植株[J].北方园艺,2014,38(12):6.
CHEN Xiao,SHENG Ping-ping,LIU Run-jin,et al.Effect of Intercropping System of Pepper-Watermelon Crops Inoculating Arbuscular Mycorrhizal Fungus on Growth and Defence Enzymes Activity of the Continuous Cropping Watermelon[J].Northern Horticulture,2014,38(07):6.
[3]张婷玉,林 多,杨延杰.辣椒根系分泌物的收集方法研究[J].北方园艺,2014,38(12):14.
ZHANG Ting-yu,LIN Duo,YANG Yan-jie.Study on Collection Method of Root Exudates on Pepper[J].Northern Horticulture,2014,38(07):14.
[4]叶 林,李春江,张光弟,等.不同育苗穴数、基质配比和施肥量对温室辣椒幼苗生长及其秧苗质量的影响[J].北方园艺,2014,38(13):50.
YE Lin,LI Chun-jiang,ZHANG Guang-di,et al.Effects of Different Seedling Number of Holes，Substrates and Fertilization on the Growth and Quality of Greenhouse Pepper Seedlings[J].Northern Horticulture,2014,38(07):50.
[5]孔小平,苗增建.等离子体处理辣椒种子对其性状及产量的影响[J].北方园艺,2013,37(13):34.
KONG Xiao-ping,MIAO Zeng-jian.Effect of Plasma Treatment on Characters and Output of Pepper Seeds[J].Northern Horticulture,2013,37(07):34.
[6]高万里.白城地区辣椒产业发展对策研究[J].北方园艺,2014,38(04):159.
GAO Wan-li.Study on the Development Countermeasure of Pepper Industry in Baicheng Area[J].Northern Horticulture,2014,38(07):159.
[7]岳振平.不同种植密度对早春大棚辣椒产量和产值的影响[J].北方园艺,2014,38(05):51.
YUE Zhen-ping.Effect of Different Planting Densty on Fruit Yield and Output Value of Pepper in Early Spring[J].Northern Horticulture,2014,38(07):51.
[8]郭亚华,谢立波,王雪,等.辣椒经地面模拟诱变后的RAPD鉴定[J].北方园艺,2014,38(05):95.
GUO Ya-hua,XIE Li-bo,WANG Xue,et al.The RAPD Detection of Capsicum annuum L. After Ground Simulation[J].Northern Horticulture,2014,38(07):95.
[9]杨飞,高艳明,李建设.宁夏设施沙培辣椒引种试验[J].北方园艺,2013,37(10):44.
YANG Fei,GAO Yan-ming,LI Jian-she.Introduction Test of Sand Culture Facilities Pepper in Ningxia[J].Northern Horticulture,2013,37(07):44.
[10]马寿宾,孙艳,王琛,等.分子标记辅助选择辣椒抗疫病新种质研究[J].北方园艺,2013,37(10):107.
MA Shou-bin,SUN Yan,WANG Chen,et al.Molecular Marker Assisted Selection of Pepper Materials with Resistance to Phytophthora Blight[J].Northern Horticulture,2013,37(07):107.
备注/Memo
第一作者简介：谢雪果(1997-),女，硕士研究生，研究方向为园艺植物逆境。E-mail：1979411935@qq.com.责任作者：吉雪花（1977-），女，博士，副教授，现主要从事蔬菜抗逆及种质创新等研究工作。E-mail:lilysnowjxh@163.com.基金项目：国家自然科学基金资助项目（32060676，31860548）。收稿日期：2021-09-17