[1]戴晓港,李淑娴*.柳树AP2/ERF基因家族全基因组鉴定和表达分析[J].江苏林业科技,2021,48(05):1-12.[doi:10.3969/j.issn.1001-7380.2021.05.001]
 Dai Xiaogang,Li Shuxian*.Genome-wide identification and characterization of the AP2/ERF gene family in willow[J].Journal of Jiangsu Forestry Science &Technology,2021,48(05):1-12.[doi:10.3969/j.issn.1001-7380.2021.05.001]
点击复制

柳树AP2/ERF基因家族全基因组鉴定和表达分析()
分享到:

《江苏林业科技》[ISSN:1001-7380/CN:32-1236/S]

卷:
第48卷
期数:
2021年05期
页码:
1-12
栏目:
试验研究
出版日期:
2021-10-31

文章信息/Info

Title:
Genome-wide identification and characterization of the AP2/ERF gene family in willow
文章编号:
1001-7380(2021)05-0001-12
作者:
戴晓港李淑娴*
南京林业大学林学院,南方杨树工程技术研究中心,江苏省杨树种质创新与品种改良重点实验室,江苏 南京 210037
Author(s):
Dai XiaogangLi Shuxian*
The Key Laboratory of Tree Genetic Improvement and Biotechnology of Jiangsu Province,The Southern Poplar Germplasm Engineering and Wood Processing Technology Center, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
关键词:
簸箕柳AP2/ERF基因家族分子进化干旱胁迫基因表达
Keywords:
Salix suchowensisAP2/ERF gene familyMolecular evolutionDrought stressGene expression
分类号:
Q756;S792.12
DOI:
10.3969/j.issn.1001-7380.2021.05.001
文献标志码:
A
摘要:
APETALA2/ethylene-responsive factor (AP2/ERF)转录因子在调控植物的生长和发育、应生物胁迫和非生物胁迫等方面扮演着至关重要的角色。该文对簸箕柳基因组中AP2/ERF基因进行查找,分析了该基因家族的保守结构域、基因结构、启动子区域顺式作用元件、基因在染色体上的分布及其在干旱胁迫下的差异表达。分析结果发现,簸箕柳中共含有208个AP2/ERF基因。根据系统发育树聚类分析的结果,这些基因可分为AP2,RAV,ERF和Soloist 4个亚类;基因结构分析表明,AP2Soloist基因内含子较多,而多数ERF和所有RAV基因都无内含子;对启动子区域顺式作用元件分析,发现簸箕柳AP2/ERF家族基因启动子区域富含响应非生物胁迫的相关元件;对基因在染色体上分布分析表明,簸箕柳AP2/ERF基因在不同染色体上分布不均匀,其中42个基因的扩张与串联复制有关。利用蒿柳杂交子代的干旱胁迫和对照样品的转录组序列进行了差异表达分析,发现了5个AP2/ERF基因在干旱胁迫下显著上调表达。分析结果为深入研究柳树AP2/ERF基因家族的功能提供了重要参考。
Abstract:
APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors perform a crucial role in various biological processes, such as regulating plant growth and development, responding to abiotic and biotic stresses. In this study, we identified AP2/ERF superfamily genes in Salix suchowensis, and analyzed their conserved motif, gene structure, cis-regulatory elements in the promoter, chromosome distribution and expression patterns under drought stress. A total of 208 AP2/ERF genes were identified in S. suchowensis genome. The identified AP2/ERF genes were classified into 4 major clades including AP2, ERF, RAV and Soloist based on the phylogenetic trees. Gene structural analysis showed that the genes in AP2 and Soloist clades had more introns than those in ERF and RAV clades. Cis-regulatory elements which are related to abiotic stresses were identified and enriched in the promotor of the SsAP2/ERF genes. Plotting their distribution showed that the SsAP2/ERFs unevenly scattered on the 19 chromosomes of S. suchowensis, with 42 (20.2%) SsAP2/ERF genes related to tandem duplication. The transcriptome reads derived from S. viminalis progeny with drought treatment were mapped on to the genome of S. suchowensis and five AP2/ERF genes were identified which were up-regulated in drought stress compared with control treatment. The above results will provide a valuable clue for further exploring the functional of willow AP2/ERF genes.

参考文献/References:

[1]PLEGUEZUELO C R R, ZUAZO V H D, BIELDERS C, et al.Bioenergy farming using woody crops. A review[J]. Agronomy for Sustainable Development,2015,35(1):95-119.
[2]ARGUS G W. Salix (Salicaceae) distribution maps and a synopsis of their classification in North America, North of Mexico[J]. Harvard Papers in Botany, 2007, 12(2):335-368.
[3]施士争,潘明建,王保松,等.培育灌木柳生物质能源林的前景[J].江苏林业科技, 2006,33(3):1-5.
[4]王保松,施士争.中国柳树种质资源[M].北京:中国林业出版社,2018.
[5]JOFUKU K D, DEN BOER B G, VAN MONTAGU M, et al. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2[J]. Plant Cell,1994,6(9):1211.
[6]AUKERMAN M J.Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes[J].The Plant Cell,2003,15(11):2730-2741.
[7]KLUCHER K M, CHOW H, REISER L, et al. The AINTEGUMENTA gene of Arabidopsis required for ovule and female gametophyte development is related to the floral homeotic gene APETALA2.[J]. Plant Cell, 1996, 8(2):137-53.
[8]GUILLAUMOT L W M A, GERMOT A, MEYTRAUD F, et al. Expression patterns of LmAP2L1 and LmAP2L2 encoding two-APETALA2 domain proteins during somatic embryogenesis and germination of hybrid larch (Larix×marschlinsii)[J]. Journal of Plant Physiology, 2008, 165(9):1003-1010.
[9]MOOSE S P, SISCO P H. Glossy15, an APETELA2-like gene from maize that regulates leaf epidermal cell identity[J]. Genes & Development, 1997, 10(23):3018-3027.
[10]HU Y X, WANG Y X, LIU X F, et al. Arabidopsis RAV1 is down-regulated by brassino steroid and may act as a negative regulator during plant development[J]. Cell Research,2004,14(1):8-15.
[11]SOHN K H, LEE S C, JUNG H W, et al. Expression and functional roles of the pepper pathogen-induced transcription factor RAV1 in bacterial disease resistance, and drought and salt stress tolerance[J]. Plant Molecular Biology, 2006, 61(6):897-915.
[12]LI X J, LI M, ZHOU Y, et al. Overexpression of cotton RAV1 gene in Arabidopsis confers transgenic plants high salinity and drought sensitivity[J]. Plos One, 2015, 10(2): e0118056.
[13]ZHANG G Y, MING C, LI L C, et al. Overexpression of the soybean GmERF3 gene, an AP2/ERF type transcription factor for increased tolerances to salt, drought, and diseases in transgenic tobacco[J]. Journal of Experimental Botany, 2009, 60(13):3781-3796.
[14]ZHU X L, QI L, LIU X, et al. The wheat ethylene response factor transcription factor pathogen-induced ERF1 mediates host responses to both the necrotrophic pathogen Rhizoctonia cerealis and freezing stresses[J]. Plant Physiology, 2014, 164(3):1499-1514.
[15]HONG J P, KIM W T. Isolation and functional characterization of the Ca-DREBLP1 gene encoding a dehydration-responsive element binding-factor-like protein 1 in hot pepper (Capsicum annuum L. cv. Pukang)[J]. Planta, 2005, 220(6):875-888.
[16]WU L, ZHANG Z, ZHANG H, et al. Transcriptional modulation of ethylene response factor protein JERF3 in the oxidative stress response enhances tolerance of tobacco seedlings to salt, drought, and freezing[J]. Plant Physiology, 2008, 148(4):1953-1963.
[17]ITO Y, KATSURA K, MARUYAMA K, et al. Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice[J]. Plant & Cell Physiology, 2006, 47(1):141-153.
[18]QIN F, KAKIMOTO M, SAKUMA Y, et al. Regulation and functional analysis of ZmDREB2A, in response to drought and heat stresses in Zea mays L[J]. Plant Journal, 2007, 50(1):54-69.
[19]WEI S, YANG Y, YIN T. The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution[J]. Horticulture research, 2020, 7(1): 1-12.
[20]张珏,黄瑞芳,韩杰峰.乔木柳4个无性系耐旱性的初步研究[J].江苏林业科技, 2020, 47(6):47-49.
[21]GUO A, HE K, LIU D, et al. DATF: a database of Arabidopsis transcription factors[J].Bioinformatics,2005,21(10): 2568-2569.
[22]LOBO. Basic local alignment search tool (BLAST)[J]. Journal of Molecular Biology, 2008, 215(3):403-410.
[23]EDDY S R. Accelerated profile HMM searches[J]. Plos Computational Biology, 2011, 7(10):e1002195.
[24]LETUNIC I, DOERKS T, BORK P. SMART: recent updates, new developments and status in 2015[J]. Nucleic Acids Research, 2015, 43(Database issue):257-260.
[25]NAKANO T, SUZUKI K, FUJIMURA T, et al. Genome-wide analysis of the ERF gene family in Arabidopsis and rice[J]. Plant Physiology, 2006, 140(2):411-432.
[26]TANG Z, BLACQUIERE G, LEUS G. Clustal W and Clustal X version 2.0[J]. Bioinformatics, 2007, 23(21):2947-2948.
[27]TAMURA K, STECHER G, PETERSON D, et al. MEGA6: Molecular evolutionary genetics analysis version 6.0[J]. Molecular Biology & Evolution, 2013, 30(12):2725-2729.
[28]CHEN C, CHEN H, ZHANG Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 2020, 13(8): 1194-1202.
[29]VOORRIPS R E. MapChart: software for the graphical presentation of linkage maps and QTLs[J]. Journal of heredity, 2002, 93(1): 77-78.
[30]LI H, DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2009, 25(14), 1754-1760.
[31]WANG L, FENG Z, WANG X, et al. DEGseq: an R package for identifying differentially expressed genes from RNA-seqdata[J]. Bioinformatics, 2010, 26(1):136-138.
[32]PUCHOLT P, SJ DIN P, WEIH M, et al. Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes[J]. BMC Plant Biology, 2015, 15(1): 1-16.
[33]ZHUANG J, CAI B, PENG R H, et al. Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa[J]. Biochemical & Biophysical Research Communications, 2008, 371(3):468-474.
[34]RAO G D, SUI J K, ZENG Y F, et al. Genome-wide analysis of the AP2/ERF gene family in Salix arbutifolia[J]. FEBS Open Bio, 2015, 5(1):132-137.
[35]LICAUSI F, GIORGI F M, ZENONI S, et al. Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera[J]. BMC Genomics, 2010, 11(1):719.
[36]LICAUSI F, OHME-TAKAGI M, PERATA P. APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs[J]. New Phytologist, 2013, 199(3):639-649.
[37]KASUGA M, MIURA S, SHINOZAKI K, et al. A combination of the Arabidopsis DREB1A gene and stress-inducible rd29A promoter improved drought-and low-temperature stress tolerance in tobacco by gene transfer[J]. Plant & Cell Physiology, 2004, 45(3):346-50.
[38]KRISHNASWAMY S, VERMA S, RAHMAN M H, et al. Functional characterization of four APETALA2-family genes (RAP2.6, RAP2.6L, DREB19 and DREB26) in Arabidopsis [J]. Plant Molecular Biology, 2011,75(1-2):107-127.

备注/Memo

备注/Memo:
收稿日期:2021-06-06;修回日期:2021-07-28
基金项目:国家自然科学基金项目“簸箕柳组培再生体系及农杆菌介导的遗传转化研究”(31500533)
作者简介:戴晓港(1984- ),男,江苏新沂人,实验师,博士。主要从事林木遗传育种研究。E-mail: xgdai@njfu.edu.cn
*通信作者:李淑娴(1969- ),女,山东烟台人,教授,博士。主要从事观赏植物育种研究。E-mail: shuxianli@njfu.com.cn
更新日期/Last Update: 2021-12-02