[1]许瑞瑞,高明刚,刘春香.苹果基因组中转录因子的鉴定与分析[J].北方园艺,2018,42(09):42-50.[doi:10.11937/bfyy.20173398]
　XU Ruirui,GAO Minggang,LIU Chunxiang.Identification and Analysis of Transcription Factors in Apple Genome[J].Northern Horticulture,2018,42(09):42-50.[doi:10.11937/bfyy.20173398]

点击复制

苹果基因组中转录因子的鉴定与分析

《北方园艺》[ISSN:1001-0009/CN:23-1247/S] 卷: 第42卷期数: 2018年09 页码: 42-50 栏目: 出版日期: 2018-04-15

Title:: Identification and Analysis of Transcription Factors in Apple Genome

作者:: 许瑞瑞; 高明刚; 刘春香; （潍坊学院生物与农业工程学院，山东省高校生物化学与分子生物学重点实验室，山东潍坊 261061）

Author(s):: XU Ruirui; GAO Minggang; LIU Chunxiang; (College of Biological and Agricultural Engineering，Weifang University/Key Laboratory of Biochemistry and Molecular Biology in Universities of Shandong，Weifang，Shandong 261061)

关键词:: 苹果; 基因组; 转录因子; 鉴定分析; 干旱

Keywords:: apple; genome; transcription factor; identification and analysis; drought

DOI:: 10.11937/bfyy.20173398

文献标志码:: A

摘要:: 转录因子是基因表达调控过程中的重要调节因子。为更好地了解蔷薇科植物苹果转录因子所编码的基因家族，利用苹果基因组数据进行转录因子筛选鉴定和系统预测，并与桃和草莓2个蔷薇科物种进行分析比较。结果表明：在苹果、桃、草莓中分别鉴定到3 039、1 527、1 506个转录因子成员，可分为58个转录因子家族；基因染色体定位显示预测的转录因子以不同密度分布在所有染色体上；所有的转录因子都具有类似的GO分析结果和亚细胞定位预测信息；随机选择了与拟南芥MYB转录因子同源性较高的苹果基因进行了干旱胁迫处理下的表达量检测，值得注意的是，有6个基因经过PEG处理后在平邑甜茶和T337苹果品种中的表达量具有相似的变化趋势。该研究系统分析鉴定苹果全基因组中的所有转录因子基因家族，为今后深入了解蔷薇科植物转录因子的分类和基因功能研究提供了一定的参考依据。

Abstract:: Transcription factors (TFs) are essential regulators of gene expression.To better understand TFs encoding genes in Rosaceae，especially in apple，a silico genomic analysis of TFs prediction was performed using apple genomes，as well as compared with peach and strawberry.The results showed that a total of 3 039，1 527 and 1 506 TFs genes were identified in apple，peach and strawberry，respectively，which could be classified into 58 families.The genomic location showed that the predicted TFs were distributed across all chromosomes with different densities.Meanwhile，all the TFs had the similar GO terms and subcellular localization information.Then，the drought-related transcription factors in apple homologous with AtMYBs were predicted and detected in Arabidopsis.Encouragingly，six of the selected genes were found to respond to PEG treatments in M.hupehensis and T337 with the similar trends.To the best of our knowledge，this was the first report of a genome-wide analysis of the TFs gene family in three rosaceous plants.This study provided valuable information for understanding the classification and putative functions of the TFs in rosaceous plant.

参考文献/References:

[1]JUNG S，MAIN D.Genomics and bioinformatics resources for translational science in Rosaceae[J].Plant Biotechnology Reports,2014(8):49-64.

[2]SHULAEV V，KORBAN S S，SOSINSKI B，et al.Multiple models for Rosaceae genomics[J].Plant Physiology,2008,147:985-1003.

[3]SHULAEV V,SARGENT D J,CROWHURST R N,et al.The genome of woodland strawberry(Fragaria vesca)[J].Nature Genetics,2011,43:109-116.

[4]VELASCO R,ZHARKIKH A,AFFOURTIT J,et al.The genome of the domesticated apple (Malus×domestica Borkh.)[J].Nature Genetics,2010,42:833-839.

[5]VERDE I,ABBOTT A G,SCALABRIN S,et al.The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity，domestication and genome evolution[J].Nature Genetics,2013,45:487-494.

[6]ALVES M S,DADALTO S P,GONCALVES A B,et al.Plant bZIP transcription factors responsive to pathogens：A review[J].International Journal of Molecular Sciences,2013(14):7815-7828.

[7]RIECHMANN J L,HEARD J,MARTIN G,et al.Arabidopsis transcription factors：Genome-wide comparative analysis among eukaryotes[J].Science,2000,290:2105-2110.

[8]ZHANG L,ZHAO G,XIA C,et al.A wheat R2R3-MYB gene，[STBX]TaMYB30-B[STBZ]，improves drought stress tolerance in transgenic Arabidopsis[J].Journal of Experimental Botany,2012,63:5873-5885.

[9]BAKSHI M,OELMULLER R.WRKY transcription factors：Jack of many trades in plants[J].Plant Signaling Behavior,2014(9):e27700.

[10]DUBOS C,STRACKE R,GROTEWOLD E,et al.MYB transcription factors in Arabidopsis[J].Trends in Plant Science,2010(15):573-581.

[11]RUSHTON D L,TRIPATHI P,RABARA R C,et al.WRKY transcription factors：Key components in abscisic acid signalling[J].Plant Biotechnology Journal,2012(10):2-11.

[12]PEREZ-RODRIGUEZ P,RIANO-PACHON D M,CORREA L G,et al.PlnTFDB：Updated content and new features of the plant transcription factor database[J].Nucleic Acids Research,2010,38:822-827.

[13]GUO A,HE K,LIU D,et al.DATF：A database of Arabidopsis transcription factors[J].Bioinformatics,2005,21:2568-2569.

[14]GAO G,ZHONG Y,GUO A,et al.DRTF：A database of rice transcription factors[J].Bioinformatics,2006(22):1286-1287.

[15]JIANG Y,ZENG B,ZHAO H,et al.Genome-wide transcription factor gene prediction and their expressional tissue-specificities in maize[J].Journal of Integrative Plant Biology,2012,54:616-630.

[16]CAO Z H,ZHANG S Z,WANG R K,et al.Genome wide analysis of the apple MYB transcription factor family allows the identification of [STBX]MdMYB121 [STBZ]gene confering abiotic stress tolerance in plants[J].PLoS One,2013(8):e69955.

[17]SU H Y,ZHANG S Z,YUAN X W,et al.Genome-wide analysis and identification of stress-responsive genes of the NAM-ATAF1，2-CUC2 transcription factor family in apple[J].Plant Physiology Biochemistry,2013(1):11-21.

[18]WANG X,ZHANG S,SU L,et al.A genome-wide analysis of the LBD (LATERAL ORGAN BOUNDARIES domain) gene family in Malus domestica with a functional characterization of [STBX]MdLBD11[STBZ][J/OL].PLoS One,2013(8):e57044.

[19]ZHAO T,LIANG D,WANG P,et al.Genome-wide analysis and expression profiling of the DREB transcription factor gene family in Malus under abiotic stress[J].Molecular Genetics and Genomics,2012,287:423-436.

[20]JUNG S,FICKLIN S P,LEE T,et al.The genome database for rosaceae (GDR)：Year 10 update[J].Nucleic Acids Research,2014,42:1237-1244.

[21]FINN R D,BATEMAN A,CLEMENTS J,et al.Pfam：The protein families database[J].Nucleic Acids Research,2014,42:D222-230.

[22]LIU R H,MENG J L.MapDraw：A microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data[J].Hereditas,2003,25:317-321.

[23]KRZYWINSKI M,SCHEIN J,BIROL I,et al.Circos：An information aesthetic for comparative genomics[J].Genome Research,2009(19):1639-1645.

[24]CONESA A,GTZ S.Blast2GO：A comprehensive suite for functional analysis in plant genomics[J].International Journal of Plant Genomics,2008:1-12.

[25]YE J,FANG L,ZHENG H,et al.WEGO：A web tool for plotting GO annotations[J].Nucleic Acids Research,2006,34:293-297.

[26]LIU Z X,LIU，S.L,YANG H Q,et al.Using protein granularity to extract the protein sequence features[J].Journal of Theoretical Biology,2013,331:48-53.

[27]KASUGA M,MIURA S,SHINOZAKI K,et al.A combination of the Arabidopsis [STBX]DREB1A[STBZ] gene and stress-inducible rd29A promoter improved drought-and low-temperature stress tolerance in tobacco by gene transfer[J].Plant Cell Physiology,2004,45:346-350.

[28]COMINELLI E,GALBIATI M,VAVASSEUR A,et al.A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance[J].Curr Biology,2005,15(13):1196-1200.

[29]PARK M Y,KANG J Y,KIM S Y.Overexpression of AtMYB52 confers ABA hypersensitivity and drought tolerance[J].Molecular Cells,2011,31(5):447-454.

[30]DING Z,LI S,AN X,et al.Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana[J].Journal of Genetics Genomics,2009,36(1):17-29.

[31]COMINELLI E,SALA T,CALVI D,et al.Over-expression of the Arabidopsis [STBX]AtMYB41 [STBZ]gene alters cell expansion and leaf surface permeability[J].Plant Journal,2008,53(1):53-64.

[32]LEE SB,KIM H,KIM R J,et al.Overexpression of Arabidopsis MYB96 confers drought resistance in Camelina sativa via cuticular wax accumulation[J].Plant Cell Reports,2014,33(9):1535-1546.

[33]XIE Z,LI D,WANG L,et al.Role of the stomatal development regulators FLP/MYB88 in abiotic stress responses[J].Plant Journal,2010,64(5):731-739.

[34]BAUMANN K,PEREZ-RODRIGUEZ M,BRADLEY D,et al.Control of cell and petal morphogenesis by R2R3 MYB transcription factors[J].Development,2007,134:1691-1701.

[35]GIGOLASHVILI T,ENGQVIST M,YATUSEVICH R,et al.HAG2/MYB76 and HAG3/MYB29 exert a specific and coordinated control on the regulation of aliphatic glucosinolate biosynthesis in Arabidopsis thaliana[J].New Phytologist,2008,177:627-642.

[36]GIGOLASHVILI T,YATUSEVICH R,BERGER B,et al.The R2R3-MYB transcription factor HAG1/MYB28 is a regulator of methionine-derived glucosinolate biosynthesis in Arabidopsis thaliana[J].Plant Journal,2007,51:247-261.

[37]VIMOLMANGKANG S,HAN Y,WEI G,et al.An apple MYB transcription factor，MdMYB3，is involved in regulation of anthocyanin biosynthesis and flower development[J].BMC Plant Biology,2013(13):176.

[38]ULKER B,SHAHID MUKHTAR M,SOMSSICH I E.The WRKY70 transcription factor of Arabidopsis influences both the plant senescence and defense signaling pathways[J].Planta,2007,226:125-137.

[39]EULGEM T,RUSHTON P J,ROBATZEK S,et al.The WRKY superfamily of plant transcription factors[J].Trends in Plant Science,2000(5):199-206.

[40]GAO J J,ZHANG Z,PENG R H,et al.Forced expression of [STBX]Mdmyb10[STBZ]，a myb transcription factor gene from apple，enhances tolerance to osmotic stress in transgenic Arabidopsis[J].Molecular Biology Reports,2011,38:205-211.

[41]DAI X,XU Y,MA Q,et al.Overexpression of an R1R2R3 MYB gene，[STBX]OsMYB3R-[STBZ]2，increases tolerance to freezing，drought，and salt stress in transgenic Arabidopsis[J].Plant Physiology,2007,143:1739-1751.

相似文献/References:

[1]曹慧,姜倩倩,张保仁,等.节水养根处理对苹果枝叶生长发育的影响[J].北方园艺,2013,37(04):1.
[2]王贵平,王金政,薛晓敏,等.叶面喷施甜菜碱对干旱胁迫下苹果幼树[J].北方园艺,2014,38(12):10.
　WANG Gui-ping,WANG Jin-zheng,XUE Xiao-min,et al.Effect of Spraying Glycinebetaine on Physiological Responses of Apple Young Trees Under Drought Stress[J].Northern Horticulture,2014,38(09):10.
[3]李莹,任亚梅,马学敏,等.1-MCP处理结合不同贮藏条件对苹果常温货架品质的影响[J].北方园艺,2014,38(11):137.
　LI Ying,REN Ya-mei,MA Xue-min,et al.Effects of 1-MCP Treatment With Different Storage Conditions on Quality of Apple During Shelf Life at Room Temperature[J].Northern Horticulture,2014,38(09):137.
[4]党建美,胡清玉,张瑜,等.炭疽菌叶枯病在我国苹果产区的发生分布及趋势分析[J].北方园艺,2014,38(10):177.
　DANG Jian-mei,HU Qing-yu,ZHANG Yu,et al.The Occurrence Trend and Distribution of Apple Glomerella Leaf Spot in China[J].Northern Horticulture,2014,38(09):177.
[5]解贝贝,沙广利,戴洪义,等.六种无融合生殖砧木对‘嘎拉’苹果果实大小和品质的影响[J].北方园艺,2013,37(17):23.
　XIE Bei-bei,SHA Guang-li,DAI Hong-yi,et al.Effect of Six No Fusion Reproductive Rootstocks on the Fruit Size and Quality of ‘Gala’ Apple[J].Northern Horticulture,2013,37(09):23.
[6]冯娟娟,刘军弟,霍学喜.世界主要落叶水果主产国生产与贸易预测分析[J].北方园艺,2014,38(04):195.
[7]吕天星,王铭,伊凯.苹果杂种实生苗叶片性状遗传趋势研究[J].北方园艺,2013,37(14):8.
　LV Tian-xing,WANG Ming,YI Kai.Study on Genetic Trends of Leaf Traits in Apple Hybrid Seedling[J].Northern Horticulture,2013,37(09):8.
[8]史星雲,王立新,王亚杰,等.陕西省苹果主栽品种品质差异及相关性分析[J].北方园艺,2013,37(14):11.
　SHI Xing-yun,WANG Li-xin,WANG Ya-jie,et al.Quality and Correlation Analysis of the Main Apple Cultivars in Shaanxi Province[J].Northern Horticulture,2013,37(09):11.
[9]隗晓雯,郭静,王菲,等.不同矮化砧木叶片酶活性与内源激素含量的差异[J].北方园艺,2013,37(14):16.
　WEI Xiao-wen,GUO Jing,WANG Fei,et al.Difference of Enzyme Activity and the Content of Endogenous Hormones in the Leaves of Different Apple Dwarfing Rootstocks[J].Northern Horticulture,2013,37(09):16.
[10]刘君,刁永强,陈淑英,等.伊犁河谷不同苹果品种苗木冻害调查及分析[J].北方园艺,2013,37(23):34.
　LIU Jun,DIAO Yong-qiang,CHEN Shu-ying,et al.An Investigation and Analysis of Freeze Injury of Different Varieties Apple Seedlings in Ili Area[J].Northern Horticulture,2013,37(09):34.

备注/Memo

第一作者简介：许瑞瑞（1982-），女，博士，副教授，研究方向为植物逆境分子生物学与基因表达调控。E-mail：xuruirui2006@163.com.基金项目：国家自然科学基金青年资助项目（31400225）；潍坊市科技发展计划资助项目（2016GX016）；山东省自然科学基金资助项目（2014ZRB01AAC）。收稿日期：2018-02-24

更新日期/Last Update: 2018-05-23