Please wait a minute...
浙江大学学报（农业与生命科学版）
Journal of Zhejiang University (Agriculture and Life Sciences)  2020, Vol. 46 Issue (6): 677-686    DOI: 10.3785/j.issn.1008-9209.2020.06.011
Quantitative genetics ＆ bioinformatics     
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
Download: HTML   HTML ( )    PDF(10617KB)
Export: BibTeX | EndNote (RIS)      

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     
Received: 01 June 2020      Published: 31 December 2020
CLC:  S 634.1  
Corresponding Authors: Guohu CHEN     E-mail: cgh@ahau.edu.cn
Service
E-mail this article
Add to my bookshelf
Add to citation manager
E-mail Alert
RSS
Articles by authors
Guohu CHEN
Hao WANG
Guang LI
Xiaoyan TANG
Chenggang WANG
Lei ZHANG
Jinfeng HOU
Lingyun YUAN
Cite this article:

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.

URL:

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


白菜PRX基因家族的鉴定与生物信息学分析

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 
Fig. 1 Chromosomal mapping of BrPRX family genes
Fig. 2 Conserved motif and gene structure analyses of BrPRX genes
Fig. 3 Phylogenetic analysis of PRX family genes from A.thaliana and B. rapa
Fig. 4 Synteny map of BrPRX family genes
Fig. 5 Synteny map of PRX family genes between A. thaliana and B. rapaChr1-5: Chromosome number of A. thaliana; A01-10: Chromosome number of B. rapa.
Fig. 6 RNA-Seq analysis of BrPRX genes in different tissues
Fig. 7 RNA-Seq analysis (A) and Venn plot (B) of BrPRX differentially expressed genes in three male sterile lines
[1]   PASSARDI F, COSIO C, PENEL C, et al. Peroxidases have more functions than a Swiss army knife. Plant Cell Reports, 2005,24(5):255-265. DOI:10.1007/s00299-005-0972-6
doi: 10.1007/s00299-005-0972-6
[2]   ALMAGRO L, GóMEZ ROS L V, BELCHI-NAVARRO S, et al. Class Ⅲ peroxidases in plant defence reactions. Journal of Experimental Botany, 2009,60(2):377-390. DOI:10.1093/jxb/ern277
doi: 10.1093/jxb/ern277
[3]   魏崃,张丽,王伟威,等.大豆过氧化物酶Ⅲ的生物信息学分析.分子植物育种,2015,13(11):2453-2460. DOI:10.13271/j.mpb.013.002453
WEI L, ZHANG L, WANG W W, et al. Bioinformatics analysis of class Ⅲ peroxidases in Glycine max. Journal of Molecular Plant Breeding, 2015,13(11):2453-2460. (in Chinese with English abstract)
doi: 10.13271/j.mpb.013.002453
[4]   高正银,孙文杰,宋晓云,等.雷蒙德棉第Ⅲ类过氧化物酶全基因组鉴定和表达分析.生物技术进展,2019,9(5):490-501. DOI:10.19586/j.2095-2341.2019.0043
GAO Z Y, SUN W J, SONG X Y, et al. Genome-wide identification and expression pattern analysis of class Ⅲ peroxidase family in Gossypium raimondii. Journal of Current Biotechnology, 2019,9(5):490-501. (in Chinese with English abstract)
doi: 10.19586/j.2095-2341.2019.0043
[5]   PASSARDI F, PENEL C, DUNAND C. Performing the paradoxical: How plant peroxidases modify the cell wall. Trends in Plant Science, 2004,9(11):534-540. DOI:10.1016/j.tplants.2004.09.002
doi: 10.1016/j.tplants.2004.09.002
[6]   WU Y S, YANG Z L, HOW J Y, et al. Overexpression of a peroxidase gene (AtPrx64) of Arabidopsis thaliana in tobacco improves plant’s tolerance to aluminum stress. Plant Molecular Biology, 2017,95(1/2):157-168. DOI:10.1007/s11103-017-0644-2
doi: 10.1007/s11103-017-0644-2
[7]   LORENTE F, LóPEZ-COBOLLO R M, CATALá R, et al. A novel cold-inducible gene from Arabidopsis, RCI3, encodes a peroxidase that constitutes a component for stress tolerance. The Plant Journal, 2002,32(1):13-24.
[8]   COEGO A, RAMIREZ V, ELLUL P, et al. The H2O2-regulated Ep5C gene encodes a peroxidase required for bacterial speck susceptibility in tomato. The Plant Journal, 2005,42(2):283-293. DOI:10.1111/j.1365-313X.2005.02372.x
doi: 10.1111/j.1365-313X.2005.02372.x
[9]   CHOI H W, KIM Y J, LEE S C. Hydrogen peroxide generation by the pepper extracellular peroxidase CaPO2 activates local and systemic cell death and defense response to bacterial pathogens. Plant Physiology, 2007,145(3):890-904. DOI:10.1104/pp.107.103325
doi: 10.1104/pp.107.103325
[10]   彭方林,王丽,穆春,等.萝卜过氧化物酶基因rsprx1对其抗氧化能力的影响.贵州农业科学,2014,42(9):40-42, 47.
PENG F L, WANG L, MU C, et al. Effect of peroxidase gene rsprx1 on antioxidant ability in Raphanus sativus. Guizhou Agricultural Sciences, 2014,42(9):40-42, 47. (in Chinese with English abstract)
[11]   TOGNOLLI M, PENEL C, GREPPIN H, et al. Analysis and expression of the class Ⅲ peroxidase large gene family in Arabidopsis thaliana. Gene, 2002,288(1/2):129-138. DOI:10.1016/S0378-1119(02)00465-1
doi: 10.1016/S0378-1119(02)00465-1
[12]   DUROUX L, WELINDER K G. The peroxidase gene family in plants: a phylogenetic overview. Journal of Molecular Evolution, 2003,57(4):397-407. DOI:10.1007/s00239-003-2489-3
doi: 10.1007/s00239-003-2489-3
[13]   CAO Y P, HAN Y H, MENG D D, et al. Structural, evolutionary, and functional analysis of the Class Ⅲ peroxidase gene family in Chinese pear (Pyrus bretschneideri). Frontiers in Plant Science, 2016,7:1874. DOI:10.3389/fpls.2016.01874
doi: 10.3389/fpls.2016.01874
[14]   WANG X W, WANG H Z, WANG J, et al. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics, 2011,43(10):1035-1039. DOI:10.1038/ng.919
doi: 10.1038/ng.919
[15]   BAIROCH A. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research, 2000,28(1):45-48. DOI:10.1093/nar/28.1.45
doi: 10.1093/nar/28.1.45
[16]   LETUNIC I, DOERKS T, BORK P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Research, 2014,43(D1):D257-D260. DOI:10.1093/nar/gku949
doi: 10.1093/nar/gku949
[17]   FINN R D, COGGILL P, EBERHARDT R Y, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research, 2016,44(D1):D279-D285. DOI:10.1093/nar/gkv1344
doi: 10.1093/nar/gkv1344
[18]   JONES P, BINNS D, CHANG H Y, et al. InterProScan5: genome-scale protein function classification. Bioinformatics, 2014,30(9):1236-1240.
[19]   TONG C B, WANG X W, YU J Y, et al. Comprehensive analysis of RNA-Seq data reveals the complexity of the transcriptome in Brassica rapa. BMC Genomics, 2013,14:689. DOI:10.1186/1471-2164-14-689
doi: 10.1186/1471-2164-14-689
[20]   ZHOU X, LIU Z Y, JI R Q, et al. Comparative transcript profiling of fertile and sterile flower buds from multiple-allele-inherited male sterility in Chinese cabbage (Brassica campestris L. ssp. pekinensis). Molecular Genetics and Genomics, 2017,292(5):967-990. DOI:10.1007/s00438-017-1324-2
doi: 10.1007/s00438-017-1324-2
[21]   CHEN G H, YE X Y, ZHANG S Y, et al. Comparative transcriptome analysis between fertile and CMS flower buds in Wucai (Brassica campestris L.). BMC Genomics, 2018,19:908. DOI:10.1186/s12864-018-5331-4
doi: 10.1186/s12864-018-5331-4
[22]   TAN C, LIU Z Y, HUANG S G, et al. Pectin methylesterase inhibitor (PMEI) family can be related to male sterility in Chinese cabbage (Brassica rapa ssp. pekinensis). Molecular Genetics and Genomics, 2018,293:343-357. DOI:10.1007/s00438-017-1391-4
doi: 10.1007/s00438-017-1391-4
[23]   TRAPNELL C, WILLIAMS B A, PERTEA G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 2010,28(5):511-515. DOI:10.1038/nbt.1621
doi: 10.1038/nbt.1621
[24]   CHEN C J, CHEN H, ZHANG Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 2020,13:009. DOI:10.1016/j.molp.2020.06.009
doi: 10.1016/j.molp.2020
[25]   GASTEIGER E, GATTIKER A, HOOGLAND C, et al. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 2003,31(13):3784-3788. DOI:10.1093/nar/gkg563
doi: 10.1093/nar/gkg563
[26]   BAILEY T L, BODEN M, BUSKE F A, et al. MEME suite: tools for motif discovery and searching. Nucleic Acids Research, 2009,37():W202-W208. DOI:10.1093/nar/gkp335
doi: 10.1093/nar/gkp335
[27]   LESCOT M, DéHAIS P, THIJS G, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 2002,30(1):325-327. DOI:10.1093/nar/30.1.325
doi: 10.1093/nar/30.1
[28]   HU B, JIN J, GUO A Y, et al. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 2015,31(8):1296-1297. DOI:10.1093/bioinformatics/btu817
doi: 10.1093/bioinformatics/btu817
[29]   WANG D P, ZHANG Y B, ZHANG Z, et al. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics, Proteomics & Bioinformatics, 2010,8(1):77-80. DOI:10.1016/S1672-0229(10)60008-3
doi: 10.1016/S1672-0229(10)60008-3
[30]   LYSAK M A, KOCH M A, PECINKA A, et al. Chromosome triplication found across the tribe Brassiceae. Genome Research, 2005,15(4):516-525. DOI:10.1101/gr.3531105
doi: 10.1101/gr.3531105
[31]   SAHA G, PARK J I, JUNG H J, et al. Genome-wide identification and characterization of MADS-box family genes related to organ development and stress resistance in Brassica rapa. BMC Genomics, 2015,16:178. DOI:10.1186/s12864-015-1349-z
doi: 10.1186/s12864-015-1349-z
[32]   TANG J, WANG F, HOU X L, et al. Genome-wide fractionation and identification of WRKY transcription factors in Chinese cabbage (Brassica rapa ssp. pekinensis) reveals collinearity and their expression patterns under abiotic and biotic stresses. Plant Molecular Biology Reporter, 2014,32(4):781-795. DOI:10.1007/s11105-013-0672-2
doi: 10.1007/s11105-013-0672-2
[33]   WANG Y, WANG Q Q, ZHAO Y, et al. Systematic analysis of maize class Ⅲ peroxidase gene family reveals a conserved subfamily involved in abiotic stress response. Gene, 2015,566(1):95-108. DOI:10.1016/j.gene.2015.04.041
doi: 10.1016/j.gene.2015.04.041
[34]   HAN Y H, DING T, SU B, et al. Genome-wide identification, characterization and expression analysis of the chalcone synthase family in maize. International Journal of Molecular Sciences, 2016,17(2):161. DOI:10.3390/ijms17020161
doi: 10.3390/ijms170
[35]   WANG Y Y, FENG L, ZHU Y X, et al. Comparative genomic analysis of the WRKYⅢ gene family in populus, grape, Arabidopsis and rice. Biology Direct, 2015,10:48. DOI:10.1186/s13062-015-0076-3
doi: 10.1186/s13062-015-0076-3
[1] Attached Table S1-2; Fig. S1 Download
[1] TAO Xiaoya, LI Jiayin, MAO Linchun. Effect of abscisic acid on wound-healing process in postharvest tomato fruit[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2016, 42(3): 321-326.
[2] YE Xinyi, ZHAO Xing, WANG Xiaopeng, ZHONG Yiming, YANG Jingping. Effects of soil Fe2+and Cd2+ on activities of antioxidant enzymes and Cd accumulation in rice plants[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2016, 42(1): 89-98.