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浙江大学学报（农业与生命科学版）
浙江大学学报（农业与生命科学版）  2020, Vol. 46 Issue (6): 677-686    DOI: 10.3785/j.issn.1008-9209.2020.06.011
数量遗传与生物信息     
白菜PRX基因家族的鉴定与生物信息学分析
陈国户(),王浩,李广,唐小燕,汪承刚,张磊,侯金锋,袁凌云
安徽农业大学园艺学院，安徽省园艺作物育种工程实验室，合肥 230036
Genome-wide identification and bioinformatics analysis of PRX gene family in Brassica rapa
Guohu CHEN(),Hao WANG,Guang LI,Xiaoyan TANG,Chenggang WANG,Lei ZHANG,Jinfeng HOU,Lingyun YUAN
Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, College of Horticulture, Anhui Agricultural University, Hefei 230036, China
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摘要：

为深入研究白菜（Brassica rapa）第Ⅲ类过氧化物酶（class Ⅲ peroxidases, PRX）家族基因（BrPRX）的相关功能，通过全基因组分析技术鉴定其家族成员，并对其进行生物信息学分析。结果表明：白菜基因组共有121个PRX基因，含有0～9个数量不等的内含子，在染色体上呈不均等分布，并有多对基因串联重复；系统进化树分析将白菜与拟南芥PRX家族基因分成5个簇；共线性与Ka/Ks分析表明，白菜和拟南芥之间有较高的同源性，且大部分BrPRX家族基因在进化中受到纯化选择；顺式作用调控元件分析发现，8个BrPRX基因与激素响应调节、光响应和抗逆等相关；此外，转录组数据表明，BrPRX基因具有组织表达特异性，且部分BrPRX基因在雄性不育材料中下调表达。上述研究结果为进一步研究白菜PRX基因功能奠定了基础。
关键词： 白菜;  过氧化物酶;  全基因组鉴定;  转录组分析    
Abstract:

In order to further study the functions of class Ⅲ peroxidase (PRX) family genes in Brassica rapa (BrPRX), the BrPRX was identified by genome-wide analysis, and its bioinformatics analysis was carried out. The results showed that there were a total of 121 BrPRX members, contained 0-9 introns, exhibited unequal distribution on chromosomes, and multiple pairs of BrPRX genes were distributed on chromosomes with tandem duplication. Phylogenetic analysis of PRX family genes from Arabidopsis thaliana and B. rapa suggested that these members could be divided into five groups. Synteny and Ka/Ks analyses demonstrated that B. rapa had a high homology with A. thaliana, and most of BrPRX family gene had undergone strong purifying selection in the evolution. The analysis of cis-acting regulatory elements of BrPRX family genes showed that they played important roles in hormone response regulation, light response and resistance to adversity. In addition, transcriptome data analysis showed that the BrPRX genes had tissue expression specificity, and some of them were down-regulated in the male sterility materials. These results lay a foundation for the further study of PRX genes’ function in B. rapa.
Key words: Brassica rapa    peroxidase    genome-wide identification    transcriptome analysis
收稿日期: 2020-06-01 出版日期: 2020-12-31
CLC:  S 634.1  
基金资助: 国家自然科学基金(31801853);高校优秀青年骨干人才培育资助项目(gxgnfx2019001);安徽省博士后基金(2019B320);安徽省自然科学基金(2008085QC156)
通讯作者: 陈国户     E-mail: cgh@ahau.edu.cn
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陈国户
王浩
李广
唐小燕
汪承刚
张磊
侯金锋
袁凌云

引用本文:

陈国户,王浩,李广,唐小燕,汪承刚,张磊,侯金锋,袁凌云. 白菜PRX基因家族的鉴定与生物信息学分析[J]. 浙江大学学报（农业与生命科学版）, 2020, 46(6): 677-686.

Guohu CHEN,Hao WANG,Guang LI,Xiaoyan TANG,Chenggang WANG,Lei ZHANG,Jinfeng HOU,Lingyun YUAN. Genome-wide identification and bioinformatics analysis of PRX gene family in Brassica rapa. Journal of Zhejiang University (Agriculture and Life Sciences), 2020, 46(6): 677-686.

链接本文:

http://www.zjujournals.com/agr/CN/10.3785/j.issn.1008-9209.2020.06.011    或    http://www.zjujournals.com/agr/CN/Y2020/V46/I6/677

图1  BrPRX家族基因的染色体定位
图2  BrPRX家族基因保守基序及基因结构分析
图3  白菜和拟南芥PRX家族基因系统进化分析
图4  BrPRX家族基因的共线性图谱
图5  白菜与拟南芥PRX家族基因的共线性图谱Chr1～5：拟南芥的染色体编号；A01～10：白菜的染色体编号。
图6  BrPRX家族基因在不同组织中的转录组表达分析
图7  BrPRX家族差异表达基因在雄性不育材料中的转录组表达（A）与维恩图（B）分析
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