基于全基因组的卷柏复苏相关AP2/ERF转录因子基因家族分析
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摘要
目的:系统解析药用植物卷柏AP2/ERF(APETALA2/Ethylene Responsive Factor)转录因子家族成员,为卷柏复苏相关分子调控机制研究奠定基础。方法:基于卷柏全基因组数据,采用BLASTP序列比对、系统发育树构建、基因表达分析等方法筛选卷柏复苏相关候选AP2/ERF转录因子基因。结果:卷柏基因组共注释到68个AP2/ERF家族,数量远少于已报道的高等植物;系统进化分析将AP2/ERF分为AP2(23)、DREB(16)、ERF(18)、RAV(8)和SOLOIST(3)亚家族,AP2/ERF结构域高度保守;17个基因与卷柏干旱及复水表型显著正相关,包括7个DREB亚家族和6个ERF亚家族成员。结论:AP2/ERF转录因子的挖掘为复苏相关的功能鉴定及分子调控机制研究提供基础。
Objective: To systematically identify the AP2/ERF transcription factor(TF)family of Selaginella tamariscina based on genome-wide strategy. Methods: Candidate AP2/ERF genes related to desiccation tolerance were selected by BLSTP,phylogenetic tree,and gene expression under drought stress. Results: In total,68 AP2/ERF genes were identified and divided into 5 subfamilies,including AP2(23 genes),DREB(16 genes),ERF(18 genes),RAV(8 genes),and SOLOIST(3 genes). The expression profile of 17 AP2/ERF genes was remarkably sensitive under dehydration and rehydration,including 7 DREB and 6 ERF subfamily genes. Conclusion: These results provided a basis for further functional characterization and regulation mechanism of candidate AP2/ERF genes related to desiccation tolerance.
Objective: To systematically identify the AP2/ERF transcription factor(TF)family of Selaginella tamariscina based on genome-wide strategy. Methods: Candidate AP2/ERF genes related to desiccation tolerance were selected by BLSTP,phylogenetic tree,and gene expression under drought stress. Results: In total,68 AP2/ERF genes were identified and divided into 5 subfamilies,including AP2(23 genes),DREB(16 genes),ERF(18 genes),RAV(8 genes),and SOLOIST(3 genes). The expression profile of 17 AP2/ERF genes was remarkably sensitive under dehydration and rehydration,including 7 DREB and 6 ERF subfamily genes. Conclusion: These results provided a basis for further functional characterization and regulation mechanism of candidate AP2/ERF genes related to desiccation tolerance.
引文
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[20]Wang C T,Liu H,Gao X S,et al.Overexpression of G10H and ORCA3 in the hairy roots of Catharanthus roseus improves catharanthine production[J].Plant Cell Rep,2010,29:887-894.
[2]Farrant J M,Moore J P.Programming desiccation-tolerance:from plants to seeds to resurrection plants[J].Curr Opin Plant Bio,2011,14(3):340-345.
[3]Vanburen R,Bryant D,Edger P P,et al.Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum[J].Nature,2015,527:508.
[4]Costa M C D,Artur M A S,Maia J,et al.A footprint of desiccation tolerance in the genome of Xerophyta viscosa[J].Nat Plants,2017,3(4):17038.
[5]Xiao L,Yang G,Zhang L,et al.The resurrection genome of Boea hygrometrica:A blueprint for survival of dehydration[J].Proc Natl Acad Sci USA,2015,112(18):5833-5837.
[6]Banks J A.Selaginella and 400 Million Years of Separation[J].Annu Rev Plant Biol,2009,60:223.
[7]Korall P,Kenrick P.The phylogenetic history of Selaginellaceae based on DNA sequences from the plastid and nucleus:extreme substitution rates and rate heterogeneity[J].Mol Phylogenet Evol,2004,31(3):852-864.
[8]中国科学院《中国植物志》编委会.中国植物志:第6卷[M].北京:科学出版社,2004:313
[9]国家药典委员会.中华人民共和国药典:一部[S].北京:中国医药科技出版社,2015:226
[10]Wang X,Chen S,Zhang H,et al.Desiccation Tolerance Mechanism in Resurrection Fern-Ally Selaginella tamariscina Revealed by Physiological and Proteomic Analysis[J].J Proteome Res,2010,9(12):6561-6577.
[11]Yobi A,Wong B W,Xu W,et al.Comparative metabolic profiling between desiccation-sensitive and desiccation-tolerant species of Selaginella reveals insights into the resurrection trait[J].Plant J,2012,72(6):983-999.
[12]Licausi F,Ohme-Takagi M,Perata P.APETALA2/Ethylene Responsive Factor(AP2/ERF)transcription factors:mediators of stress responses and developmental programs[J].New Phytol,2013,199(3):639-649.
[13]季爱加,罗红梅,徐志超,等.药用植物转录因子AP2/ERF研究与展望[J].科学通报,2015(14):1272-1284.
[14]Sakuma Y,Liu Q,Dubouzet J G,et al.DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs,transcription factors involved in dehydration-and cold-inducible gene expression[J].Biochem Biophys Res Commun,2002,290(3):998-1009.
[15]Nakano T,Suzuki K,Fujimura T,et al.Genome-wide analysis of the ERF gene family in Arabidopsis and rice[J].Plant Physiol,2006,140:411-432.
[16]Licausi F,Giorgi F M,Zenoni S,et al.Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera[J].BMC Genomics,2010,11:719.
[17]Ji A J,Luo H M,Xu Z C,et al.Genome-wide identification of the AP2/ERF gene family involved in active constituent biosynthesis in Salvia miltiorrhiza[J].Plant Genome,2016,9(2):1-11.
[18]Trapnell C,Roberts A,Goff L,et al.Differential gene and transcript expression analysis of RNA-seq experiments with Top Hat and Cufflinks[J].Nat Protoc,2012,7:562-578.
[19]Li X,Zhang D,Gao B,et al.Transcriptome-wide identification,classification,and characterization of AP2/ERF family genes in the desert moss Syntrichia caninervis[J].Front in Plant Sci,2017,8(47):262.
[20]Wang C T,Liu H,Gao X S,et al.Overexpression of G10H and ORCA3 in the hairy roots of Catharanthus roseus improves catharanthine production[J].Plant Cell Rep,2010,29:887-894.