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 |
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
|
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
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|