[1]张小雪,韦晓霞,陈发兴.基于转录组的百香果ARF基因家族的鉴定及表达分析[J].福建农林大学学报(自然科学版),2021,50(02):236-243.[doi:10.13323/j.cnki.j.fafu(nat.sci.).2021.02.013]
 ZHANG Xiaoxue,WEI Xiaoxia,CHEN Faxing.Transcriptome data-based identification and expression profiling of the auxin response factor(ARF)gene family in Passiflora edulia Sims[J].,2021,50(02):236-243.[doi:10.13323/j.cnki.j.fafu(nat.sci.).2021.02.013]
点击复制

基于转录组的百香果ARF基因家族的鉴定及表达分析()
分享到:

福建农林大学学报(自然科学版)[ISSN:1671-5470/CN:35-1255/S]

卷:
50卷
期数:
2021年02期
页码:
236-243
栏目:
生命科学
出版日期:
2021-02-15

文章信息/Info

Title:
Transcriptome data-based identification and expression profiling of the auxin response factor(ARF)gene family in Passiflora edulia Sims
文章编号:
1671-5470(2021)02-0236-08
作者:
张小雪1 韦晓霞2 陈发兴1
1.福建农林大学园艺学院,福建 福州 350002; 2.福建省农业科学院果树研究所,福建 福州 350013
Author(s):
ZHANG Xiaoxue1 WEI Xiaoxia2 CHEN Faxing1
1.College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; 2.Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
关键词:
百香果 ARF 基因家族 转录组 表达分析
Keywords:
passion fruit auxin response factor gene family transcriptome expression analysis
分类号:
S663.9
DOI:
10.13323/j.cnki.j.fafu(nat.sci.).2021.02.013
文献标志码:
A
摘要:
基于转录组数据对百香果ARF基因家族(PeARFs)进行鉴定,利用生物信息学软件分析其编码蛋白的理化性质、保守结构域、保守基序、系统进化情况,同时比较了它们在’福建3号’(黄果)和’福建1号’(紫果)不同果实成熟阶段的表达差异.共鉴定得到13个PeARF成员,其编码的蛋白质含有365~970个氨基酸,分子质量约为39.95~106.33 ku,等电点为5.40~8.94.保守结构域分析结果显示,所有PeARF蛋白质均具有典型的B3和Auxin-resp结构域,仅4个成员(PeARF6、PeARF8、PeARF12、PeARF13)具有Aux/IAA 结构域.保守基序分析表明,PeARFs共包含15个保守基序,每个成员包含保守基序类型和数目不同.亚细胞定位预测结果显示,13个PeARFs均定位于细胞核.系统进化分析结果显示,PeARFs蛋白可分为4个亚家族.13个PeARFs基因在果实不同发育期呈现一定的时间和品种表达特异性,其中PeARF1、PeARF6、PeARF7、PeARF8和PeARF10在两品种中的表达均随着果实的成熟而下降,而PeARF12则随着果实的成熟而上升.本研究表明PeARFs家 族中的部分成员可能与果实的成熟密切相关,结果可为进一步揭示百香果ARF基因的功能提供依据.
Abstract:
Auxin response factor(ARF)is a kind of transcription factor that locates in the promoter region of the auxin responsive genes. ARF can specifically recognize and bind to the auxin response elements and plays important roles in regulating the expression of the target genes. Based on our previous transcriptome data, the ARF gene family members of passion fruits were identified. Then their physiochemical properties, protein conserved domain, conserved motifs and evolutionary relationship were elucidated using bioinformatics analysis. Moreover, their expression patterns in ’Fujian No. 3’(yellow fruit)and ’Fujian No. 1’(purple fruit)at different ripening stages were compared. A total of 13 ARF gene family members were identified. The proteins they encoded consisted of 365-970 amino acids, with the relative molecular weight varying from 39.95 to 106.33 ku and the isoelectric point ranging between 5.40 and 8.94. Conservative domain analysis showed that all PeARF proteins contained the typical B3 and the Auxin-resp domain, and only 4 members(PeARF6, PeARF8, PeARF12 and PeARF13)contained the AUX/IAA domain. Conservative motif analysis results showed that there are 15 motifs in PeARFs, but the type and number of the conserved motifs varied among the gene family members. Subcellular localization prediction results showed that 13 PeARF proteins were localized in the nucleus. Phylogenetic analysis revealed that the PeARF gene family could be further divided into 4 subfamilies. The 13 PeARFs genes showed some temporal and variety-specific expression at different fruit ripening stages. Among them, the expression levels of PeARF1, PeARF6, PeARF7, PeARF8 and PeARF10 decreased as fruit ripened in both varieties, while the PeARF12 showed an upward trend. These findings indicate that some PeARFs(PeARF1, PeARF6, PeARF7, PeARF8, PeARF10 and PeARF12)may be closely related to fruit ripening, which provides the basis for a future study on the function of AFR genes in passion fruit.

参考文献/References:

[1] WOODWARD A W, BARTEL B. Auxin: regulation, action, and interaction[J]. Ann Bot, 2005,95(5):707-735.
[2] FLEMING A J. Plant signalling: the inexorable rise of auxin[J]. Trends Cell Biol, 2006,16(8):397-402.
[3] LI S B, XIE Z Z, HU C G, et al. A review of auxin response factors(ARFs)in plants[J]. Front Plant Sci, 2016,7:47-55.
[4] HAGEN G, GUILFOYLE T. Auxin-responsive gene expression: genes, promoters and regulatory factors[J]. Plant Mol Biol, 2002,49(3/4):373-385.
[5] 王矢乔.草莓ARF基因家族启动子预测及ARF4启动子的转录活性分析[D].沈阳:沈阳农业大学,2018.
[6] LISCUM E, REED J W. Genetics of Aux/IAA and ARF action in plant growth and development[J]. Plant Mol Biol, 2002,49(3/4):387-400.
[7] KIM J, HARTER K, THEOLOGIS A. Protein-protein interactions among the Aux/IAA proteins[J]. Proc Natl Acad Sci USA, 1997,94(22):11786-11791.
[8] SHEN C J, YUE R Q, SUN T, et al. Genome-wide identification and expression analysis of auxin response factor gene family in Medicago truncatula[J]. Frontiers in Plant Science, 2015,6:73.
[9] ELLIS C M, NAGPAL P, YOUNG J C, et al. Auxin Response Factor1 and Auxin Response Factor2 regulate senescence and floral organ abscission in Arabidopsis thaliana[J]. Development, 2005,132(20):4563-4574.
[10] OKUSHIMA Y, OVERVOORDE P J, ARIMA K, et al. Functional genomic analysis of the Auxin Response Factor gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19[J]. Plant Cell, 2005,17(2):444-463.
[11] WU M F, TIAN Q, REED J W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction[J]. Development, 2006,133(21):4211-4218.
[12] WILMOTH J C, WANG S, TIWARI S B, et al. NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation[J]. Plant J, 2005,43(1):118-130.
[13] SHEN C, WANG S, ZHANG S, et al. OsARF16, a transcription factor, is required for auxin and phosphate starvation response in rice(Oryza sativa L.)[J]. Plant Cell Environ, 2013,36(3):607-620.
[14] ZHANG S, WANG S, XU Y, et al. The auxin response factor, OsARF19, controls rice leaf angles through positively regulating OsGH3-5 and OsBRI1[J]. Plant, Cell & Environment, 2014,38(4):638-654.
[15] 胡晓,侯旭,袁雪,等.ARF和Aux/IAA调控果实发育成熟机制研究进展[J].生物技术通报,2017,33(12):37-44.
[16] WU J, WANG F, CHENG L, et al. Identification, isolation and expression analysis of auxin response factor(ARF)genes in Solanum lycopersicum[J]. Plant Cell Reports, 2011,30(11):2059-2073.
[17] HAO Y, HU G, BREITEL D, et al. Auxin response factor SlARF2 is an essential component of the regulatory mechanism controlling fruit ripening in tomato[J]. Plos Genetics, 2015,11(12):e1005649.
[18] SAGAR M, CHERVIN C, MILA I, et al. S1ARF4, an auxin response factor involved in the control of sugar metabolism during tomato fruit development[J]. Plant Physiology, 2013,161(3):1362-1374.
[19] DE JONG M, WOLTERS ARTS M, SCHIMMEL B C J, et al. Solanum lycopersicum Auxin Response Factor 9 regulates cell division activity during early tomato fruit development[J]. Journal of Experimental Botany, 2015,66(11):3405-3416.
[20] 刘松瑜,闫艳秋,冯秋硕,等.番茄生长素响应因子基因SlARF12在果实发育过程中的功能分析[J].园艺学报,2018,45(4):678-690.
[21] 梅丽华.生长素响应因子基因SlARF10在番茄果实发育过程中的功能研究[D].重庆:重庆大学,2017.
[22] GALEANO MENDOZA C H, CERNSOUZA I, ARANGO L V. Agronomic evaluation of a colombian passion fruit(Passiflora edulis Sims)germplasm collection[J]. Agronomy Research, 2018,16(4):1649-1659.
[23] TU S, XUE Y, ZHENG C, et al. Detection of passion fruits and maturity classification using Red-Green-Blue depth images[J]. Biosystems Engineering, 2018,175:156-167.
[24] DHARMASIRI N, ESTELLE M. Auxin signaling and regulated protein degradation[J]. Plant Science, 2004,9(6):302-308.
[25] TANG Y, BAO X, LIU K, et al. Genome-wide identification and expression profiling of the auxin response factor(ARF)gene family in physic nut[J]. PloS ONE, 2018,13(8):e0201024.
[26] ZHANG Y, ZENG Z, CHEN C, et al. Genome-wide characterization of the auxin response factor(ARF)gene family of litchi(Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission[J]. Peer J, 2019,7:e6677.
[27] LI H, RAN K, SUN Q. Genome-wide identification and expression analysis of peach auxin response factor gene families[J]. Journal of Plant Biochemistry and Biotechnology, 2016,25(4):349-357.
[28] KALLURI U C, DIFAZIO S P, BRUNNER A M, et al. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa[J]. BMC Plant Biol, 2007,7(1):59.
[29] WANG D, PEI K, FU Y, et al. Genome-wide analysis of the auxin response factors(ARF)gene family in rice(Oryza sativa)[J]. Gene, 2007,394(1/2):13-24.
[30] WAN S, LI W, ZHU Y, et al. Genome-wide identification, characterization and expression analysis of the auxin response factor gene family in Vitis vinifera[J]. Plant Cell Rep, 2014,33(8):1365-1375.
[31] KUMAR R, TYAGI A K, SHARMA A K. Genome-wide analysis of auxin response factor(ARF)gene family from tomato and analysis of their role in flower and fruit development[J]. Molecular Genetics and Genomics, 2011,285(3):245-260.
[32] 袁静贤.生长素相关转录因子家族基因在西瓜果实膨大过程中的调控作用分析[D].武汉:华中农业大学,2015.
[33] HARDTKE C S, BERLETH T. The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development[J]. EMBO Journal, 1998,17(5):1405-1411.
[34] PEKKER I, ALVAREZ J P, ESHED Y. Auxin response factors mediate Arabidopsis organ asymmetry via modulation of KANADI activity[J]. Plant Cell, 2005,17(11):2899-2910.
[35] WANG J W, WANG L J, MAO Y B, et al. Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis[J]. Plant Cell, 2005,17(8):2204-2216.
[36] YANG J, TIAN L, SUN M X, et al. AUXIN RESPONSE FACTOR17 is essential for pollen wall pattern formation in Arabidopsis[J]. Plant Physiol, 2013,162(2):720-731.

备注/Memo

备注/Memo:
收稿日期:2020-07-27 修回日期:2020-10-09
基金项目:农业五新项目(K6018203A); 中央引导地方科技发展专项(2017L3001); 福建省地方科技发展专项(HKH190278A); 校创新发展基金(KF2015054).
作者简介:张小雪(1996-),女.研究方向:果树生理与分子生物学.Email:13647152752@139.com.通信作者陈发兴(1967-),男,研究员,博士.研究方向:园艺植物生理与生物技术.Email:cfaxing@126.com.
更新日期/Last Update: 2021-02-15