[1]王新亮,彭玲,王健,等.苹果Dof转录因子生物信息学及其表达分析[J].江苏农业学报,2021,(02):480-492.[doi:doi:10.3969/j.issn.1000-4440.2021.02.026]
　WANG Xin-liang,PENG Ling,WANG Jian,et al.Bioinformatics and expression analysis of the Dof transcription factors in apple[J].,2021,(02):480-492.[doi:doi:10.3969/j.issn.1000-4440.2021.02.026]
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苹果Dof转录因子生物信息学及其表达分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2021年02期
页码:
480-492
栏目:
园艺
出版日期:
2021-04-30

文章信息/Info

Title:
Bioinformatics and expression analysis of the Dof transcription factors in apple
作者:
王新亮1; 2;  彭玲2;  王健1;  贾晶晶1;  唐立平1
（1.滨州学院《滨州学院学报》编辑部，山东滨州256603；2.滨州学院山东省黄河三角洲生态环境重点实验室，山东滨州256603）
Author(s):
WANG Xin-liang1; 2; PENG Ling2; WANG Jian1; JIA Jing-jing1; TANG Li-ping1
(1.Editorial Department of Journal of Binzhou University, Binzhou University, Binzhou 256603, China;2.Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou 256603, China)
关键词:
苹果; Dof基因; 转录因子; 表达分析; 生物信息学
Keywords:
apple; Dof gene; transcription factor; expression analysis; bioinformatics
分类号:
S661.1
DOI:
doi:10.3969/j.issn.1000-4440.2021.02.026
文献标志码:
A
摘要:
为了解苹果Dof转录因子家族的生物学信息与功能，利用苹果基因组GDDH13 v1.1检索及RNA-seq转录本重构找到51个Dof 基因，并通过 Pfam 和SMART检测确认，进一步对这些Dof基因进行全面分析。结果表明，除MD07G1265700外，其他50个Dof蛋白均含有一个明显的Dof结构域，且有一个CX2CX21CX2C基序。这些Dof基因编码氨基酸数为163～523，相对分子质量为18 210～55 800，等电点为5.01～10.30，多数Dof成员定位于细胞核中， 少数定位于叶绿体或线粒体中。组织特异表达显示多数Dof 基因在营养器官中的表达量高于生殖器官，而MD01G1084700、MD07G1153300、MD08G1040100、MD15G1034500基因在未成熟的果肉中表达量最高。盐碱胁迫下，除MD05G1023800基因没有检测到表达外，其他Dof基因的表达均受盐碱胁迫影响，只是响应强度和时间有差异，基因表达显著上调的有7个，显著下调的有15个。该研究结果为进一步揭示苹果Dof转录因子生物功能奠定了理论基础。
Abstract:
In order to understand the biological information and function of apple Dof transcription factor family, 51 Dof genes were found by searching apple genome GDDH13 v1.1 and RNA-seq transcripts reconstruction, and they were confirmed as members of Dof transcription factor family by Pfam and SMART detection. The Dof genes were generally analyzed furtherly. The results showed that, besides MD07G1265700, the other 50 Dof proteins all contained an obvious Dof domain and a CX2CX21CX2C motif. The number of amino acids encoded by Dof gene ranged from 163 to 523, and the relative molecular weight ranged from 18 210 to 55 800, while the isoelectric point ranged from 5.01 to 10.30. Most of the Dof proteins were located in the nucleus, and a few of them were located in the chloroplast or mitochondria. The results of tissue-specific expression showed that the expression level of most of the Dof genes expressed in vegetative organs were higher than in reproductive organs, while the expression levels of MD01G1084700, MD07G1153300, MD08G1040100 and MD15G1034500 were the highest in immature fruit flesh. Under saline-alkali stress, except for MD05G1023800 gene, the expression of other Dof genes were affected by saline-alkali stress, but the intensity and time of response were different. There were seven Dof genes significantly up-regulated and 15 Dof genes significantly down regulated. The research results lay a theoretical foundation for further study on the biological function of Dof transcription factor in apple.

参考文献/References:

[1]张婷婷,康慧,付璐璐,等. 苹果MdCYP707A家族基因表达分析和MdCYP707A1的功能鉴定[J]. 园艺学报, 2019, 46(8): 1429-1444.
[2]UMEMURA Y, ISHIDUKA T, YAMAMOTO R, et al. The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 Zn finger domain[J]. The Plant Journal, 2004, 37 (5): 741-749.
[3]MARZABAL P, GAS E, FONTANET P, et al. The maize Dof protein PBF activates transcription of γ-zein during maize seed development[J]. Plant Molecular Biology, 2008, 67 (5): 441-454.
[4]TOKUNAGA S, SANDA S, URAGUCHI Y, et al. Overexpression of the DOF-Type transcription factor enhances lipid synthesis in Chlorella vulgaris[J]. Applied Biochemistry and Biotechnology, 2019, 189(1): 116-128.
[5]KURAI T, WAKAYAMA M, ABIKO T, et al. Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions[J]. Plant Biotechnology Journal, 2011, 9 (8): 826-837.
[6]李娅,丁文杰,江海燕,等. Dof基因家族调节植物生长发育功能的研究进展[J]. 西北植物学报, 2018, 38(9): 1758-1766.
[7]YANAGISAWA S. The Dof family of plant transcription factors[J]. Trends in Plant Science, 2002, 7(12): 555-560.
[8]SHAW L M, MCINTYRE C L, GRESSHOFF P M, et al. Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation[J]. Functional & Integrative Genomics, 2009, 9(4): 485-498.
[9]GUO Y, QIU L J. Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics[J]. PLoS One, 2013, 8(9): e76809.
[10]LIJAVETZKY D, CARBONERO P, VICENTE-CARBAJOSA J. Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families[J]. BMC Evolutionary Biology, 2003, 3(1): 17.
[11]JUNG S, LEE T, CHENG C H, et al. 15 years of GDR: New data and functionality in the Genome Database for Rosaceae[J]. Nucleic Acids Research, 2019, 47(D1): D1137-D1145.
[12]KANG Y J, YANG D C, KONG L, et al. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features[J]. Nucleic Acids Research, 2017, 45(W1): W12-W16.
[13]EL-GEBALI S, MISTRY J, BATEMAN A, et al. The Pfam protein families database in 2019[J]. Nucleic Acids Research, 2019, 47(D1): D427-D432.
[14]GASTEIGER E, HOOGLAND C, GATTIKER A, et al. Protein identification and analysis tools on the ExPASy server[M]New Jersey: Humana Press, 2005: 571-607.
[15]KATOH K, ROZEWICKI J, YAMADA K D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization[J]. Briefings in Bioinformatics, 2019, 20(4): 1160-1166.
[16]SUBRAMANIAN B, GAO S, LERCHER M J, et al. Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees[J], Nucleic Acids Research, 2019, 47(W1): W270-W275.
[17]HU B, JIN P, GUO A Y, et al. GSDS 2.0: an upgraded gene feature visualization server[J]. Bioinformatics, 2015, 31(8): 1296-1297.
[18]BAILEY T L ， ELKAN C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers[C]// ALTMAN R, BRUTLAG D, KARP P, et al. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. Menlo Park, California: AAAI Press,1994: 28-36.
[19]DA L L, LIU Y, YANG J T, et al. AppleMDO: a multi-dimensional omics database for apple co-expression networks and chromatin states[J]. Frontiers in Plant Science, 2019（10）: 1333.
[20]EWAS M, KHAMES E, ZIAF K, et al. The tomato DOF daily fluctuations 1, TDDF1 acts as flowering accelerator and protector against various stresses[J]. Scientific Reports, 2017（7）: 10299.
[21]CORRALES A R, CARRILLO L, LASIERRA P, et al. Multifaceted role of cycling DOF factor 3 (CDF3) in the regulation of flowering time and abiotic stress responses in Arabidopsis[J]. Plant Cell and Environment, 2017, 40 (5): 748-764.
[22]XU P P, CHEN H Y, YING L, et al. At DOF5.4/OBP4, a DOF transcription factor gene that negatively regulates cell cycle progression and cell expansion in Arabidopsis thaliana[J]. Scientific Reports, 2016（6）: 27705.
[23]李辉,黄蔚,刘志薇,等. 茶树两个Dof 转录因子的分离及其在温度胁迫中的响应分析[J]. 茶叶科学, 2016, 36(3): 312-322.
[24]王海波,唐利洲. 基于基因组鉴定小桐子Dof 转录因子家族及其表达分析[J]. 分子植物育种, 2018, 16(3): 764-771.
[25]刘蓓,邱爽,何佳琦,等. 8个大豆Dof转录因子的生物信息学分析及干旱诱导表达[J]. 大豆科学, 2020, 39(3): 377-383.
[26]程冬梅,邓志勇,郭霭光. 小麦高分子量麦谷蛋白亚基等电点的特性分析[J]. 西北植物学报, 2006, 26(3): 532-536.
[27]GABRIELE S, RIZZA A, MARTONE J, et al. The Dof protein DAG1 mediates PIL5 activity on seed germination by negatively regulating GA biosynthetic gene AtGA3ox1[J]. The Plant Journal, 2010, 61(2): 312-323.
[28]GUALBERTI G, PAPI M, BELLUCCI L, et al. Mutations in the Dof zinc finger genes DAG2 and DAG1 influence with opposite effects the germination of Arabidopsis seeds[J]. The Plant Cell, 2002, 14(6): 1253-1263.
[29]SONG Y H, SMITH R W, TO B J, et al. FKF1 conveys crucial timing information for CONSTANS stabilization in the photoperiodic flowering[J]. Science, 2012, 336(6084): 1045-1049.
[30]FORNARA F, PANIGRAHI K C S, GISSOT L, et al. Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response[J]. Developmental Cell, 2009, 17(1): 75-86.
[31]TSUJIMOTO-INUI Y, NAITO Y, SAKURAI N, et al. Functional genomics of the Dof transcription factor family genes in suspension-cultured cells of Arabidopsis thaliana[J]. Plant Biotechnology, 2009（26）: 15-28.
[32]SKIRYCZ A, RADZIEJWOSKI A, BUSCH W, et al. The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana[J]. The Plant Journal , 2008，56（5）: 779-792.
[33]裴徐梨，荆赞革，徐境，等. 青花菜BoDof5.3基因的克隆及渍水胁迫表达特征分析[J].江苏农业学报，2020,36(6):1498-1502.
[34]韩利红，刘潮，张维维，等. 铁皮石斛热激转录因子（Hsf）基因家族鉴定及生物信息学分析[J]. 南方农业学报，2019,50(4):677-684.
[35]庞文玉，王安，杨宝谊，等. 大白菜ENT基因家族的鉴定与生物信息学分析[J].江苏农业科学，2019, 47(12):52-57.
[36]杨冬静,孙厚俊,谢逸萍,等. 甘薯等8种植物JAZ1基因的生物信息学分析[J].江苏农业学报,2019,35(5):1021-1027.
[37]唐跃辉,包欣欣,王健,等. 小桐子Dof基因家族生物信息学与表达分析[J]. 江苏农业学报, 2019, 35(1): 15-25.
[38]SADDEE A A, MALVANKAR M R, KUMAR K. Selection of reference genes for quantitative real-time PCR analysis in halophytic plant Rhizophora apiculata[J]. The Journal of Life and Environmental Sciences, 2018, 6(8): e5226.
[39]KANG H G， SINGH K B. Characterization of salicylic acid-responsive, Arabidopsis Dof domain proteins: overexpression of OBP3 leads to growth defects[J]. The Plant Journal, 2000，21（4）: 329-339.
[40]SKIRYCZ A, REICHELT M, BUROW M, et al. DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis[J]. The Plant Journal, 2006，47（1）: 10-24.

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备注/Memo

备注/Memo:
收稿日期：2020-07-13基金项目：滨州学院博士学位人员及具有硕士学位的高级职称人员科研启动费项目（2019Y36）作者简介：王新亮(1983-)，男，山东宁津人，博士，高级工程师，主要从事果树抗逆及氮素吸收利用研究。(E-mail)wiln1@163.com
更新日期/Last Update: 2021-05-10