甘蓝型油菜全基因组DELLA蛋白基因家族的鉴定和表达分析
|
摘要
DELLA蛋白是参与赤霉素调控途径的关键因子,对调节植物的生长发育具有重要的作用。为了揭示甘蓝型油菜中DELLA蛋白家族的分布和特征,利用生物信息学分析了家族成员、序列特征、进化关系和组织表达。结果表明,甘蓝型油菜中有13个DELLA蛋白基因,被定位到8条染色体和2条随机序列(chr C09_random和chr Cnn_random)上;系统进化树分析发现,该家族被聚为4个亚家族,第一亚家族含有7个基因,第二、三和四亚家族各包括2个基因; DELLA基因呈组织特异性表达,其中Bna A10g17240D、Bna C09g40420D、Bna Cnng68300D和Bna C05g47760D在各组织中表达都相对较高,在茎中Bna A06g34810D、Bna A09g18700D和Bna C09g52270D表达最高。本研究为后续基因的功能研究提供参考。
DELLA protein is a key factor involved in GA regulatory pathways and plays an important role in regulating plant growth and development.In order to reveal the distribution and characteristics of DELLA protein family in Brassica napus,family members,sequence characteristics,evolutionary relationships and tissue expression were analyzed using bioinformatics.The results showed that there were 13 DELLA protein genes in B.napus,located on 8 chromosomes with 2 random sequences(chrC09_random and chrCnn_random).The phylogenetic tree showed that the family was clustered into 4 subfamilies.The first subfamily contains 7 genes,and the second,third and fourth subfamilies each included 2 genes.The expression analysis of different tissues showed tissue-specific expression in each tissue,and BnaA10 g17240 D,BnaC09 g40420 D,BnaCnng68300 D and BnaC05 g47760 D were relatively high in each tissue.Among the stems,BnaA06 g34810 D,BnaA09 g18700 D and BnaC09 g52270 D had the highest expression.This study provided a reference for gene function reseach in the future.
DELLA protein is a key factor involved in GA regulatory pathways and plays an important role in regulating plant growth and development.In order to reveal the distribution and characteristics of DELLA protein family in Brassica napus,family members,sequence characteristics,evolutionary relationships and tissue expression were analyzed using bioinformatics.The results showed that there were 13 DELLA protein genes in B.napus,located on 8 chromosomes with 2 random sequences(chrC09_random and chrCnn_random).The phylogenetic tree showed that the family was clustered into 4 subfamilies.The first subfamily contains 7 genes,and the second,third and fourth subfamilies each included 2 genes.The expression analysis of different tissues showed tissue-specific expression in each tissue,and BnaA10 g17240 D,BnaC09 g40420 D,BnaCnng68300 D and BnaC05 g47760 D were relatively high in each tissue.Among the stems,BnaA06 g34810 D,BnaA09 g18700 D and BnaC09 g52270 D had the highest expression.This study provided a reference for gene function reseach in the future.
引文
[1] Daviere J M,Achard P. Gibberellin signaling in plants[J]. Development,2013,140(6):1147-1151.
[2] Li W J,Zhang J X,Sun H Y,et al. FveRGA1,encoding a DELLA protein,negatively regulates runner production in Fragaria vesca[J]. Planta,2018,247(4):941-951.
[3]李威,李国瑞,黄凤兰,等. DELLA家族蛋白研究进展[J].安徽农业科学,2016,44(32):147-148.
[4] Zhao X Y,Zhu D F,Zhou B,et al. Over-expression of the At GA2ox8 gene decreases the biomass accumulation and lignification in rapeseed(Brassica napus L.)[J]. J Zhejiang Univ Sci B,2010,11(7):471-481.
[5] Peng J R,Richards D E,Hartley N M,et al.‘Green revolution’ genes encode mutant gibberellin response modulators[J]. Nature,1999,400(6741):256-261.
[6] Pearce S,Saville R,Vaughan S P,et al. Molecular characterization of Rht-1 dwarfing genes in hexaploid wheat[J]. Plant Physiol,2011,157(4):1820-1831.
[7] Chen J H,Cheng T L,Wang P K,et al. Genome-wide bioinformatic analysis of DELLA-family proteins from plants[J]. Plant Omics,2013,6(3):201-207.
[8] Davière J M,Achard P. A pivotal role of DELLAs in regulating multiple hormone signals[J]. Mol Plant,2016,9(1):10-20.
[9] Tyler L. DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis[J].Plant Physiol,2004,135(2):1008-1019.
[10]陈宇杰,刘飞,梁菲菲,等.蓖麻DELLA蛋白家族GAI基因克隆、表达及生物信息学分析[J].内蒙古民族大学学报(自然科学版),2017,32(4):320-327.
[11]张文颖,王晨,朱旭东,等.葡萄全基因组DELLA蛋白基因家族鉴定及其应答外源赤霉素调控葡萄果实发育的特征[J].中国农业科学,2018,51(16):3130-3146.
[12] Gao Y,Chen J M,Zhao Y,et al. Molecular cloning and expression analysis of a RGA-like gene responsive to plant hormones in Brassica napus[J]. Mol Biol Rep,2012,39(2):1957-1962.
[13] Sun T P. Gibberellin-GID1-DELLA:A pivotal regulatory module for plant growth and development[J].Plant Physiol,2010,154(2):567-570.
[14] Murase K,Hirano Y,Sun T P,et al. Gibberellin-induced DELLA recognition by the gibberellin receptor GID1[J]. Nature,2008,456(7221):459-463.
[15] Fu X. Gibberellin-mediated proteasome-dependent degradation of the barley DELLA protein SLN1 repressor[J]. Plant Cell Online,2002,14(12):3191-3200.
[16] Ueguchi-Tanaka M,Nakajima M,Katoh E,et al. Molecular interactions of a soluble gibberellin receptor,GID1,with a rice DELLA protein,SLR1,and gibberellin[J]. Plant Cell Online,2007,19(7):2140-2155.
[17] Zhao B,Li H T,Li J J,et al. Brassica napus DS-3,encoding a DELLA protein,negatively regulates stem elongation through gibberellin signaling pathway[J]. Theor Appl Genet,2017,130(4):727-741.
[18] Li H T,Wang B,Zhang Q H,et al. Genome-wide analysis of the auxin/indoleacetic acid(Aux/IAA)gene family in allotetraploid rapeseed(Brassica napus L.)[J]. BMC Plant Biol,2017,17:204.
[19] Tamura K,Stecher G,Peterson D,et al. MEGA6:molecular evolutionary genetics analysis version 6. 0[J].Mol Biol Evol,2013,30(12):2725-2729.
[20]李晓康,刘红芳,刘婧琳,等.油菜miR156基因家族及其靶基因生物信息学分析及鉴定[J].中国油料作物学报,2018,40(2):163-173.
[21]李春金,郭媛媛,杨启航,等.甘蓝型油菜HMG基因家族的生物信息学分析[J].中国油料作物学报,2018,40(3):318-325.
[22] Wang D P,Wan H L,Zhang S,et al.Γ-MYN:a new algorithm for estimating Ka and Ks with consideration of variable substitution rates[J]. Biol Direct,2009,4(1):20.
[23] Chalhoub B,Denoeud F,Liu S Y,et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J]. Science,2014,345(6199):950-953.
[24] Wu D C,Yao J,Ho K S,et al. Limitations of alignment-free tools in total RNA-seq quantification[J].BMC Genomics,2018,19(1):1-14.
[25]夏胜前,张毅,涂金星.油菜重要性状功能基因研究进展[J].中国油料作物学报,2018,40(5):656-663.
[26] Du H Y,Yang C,Ding G D,et al. Genome-wide identification and characterization of SPX domain-containing members and their responses to phosphate deficiency in Brassica napus[J]. Front Plant Sci,2017,8:35.
[27] Chen H F,Zhang Q,He M L,et al. Molecular characterization of the genome-wide BOR transporter gene family and genetic analysis of Bna C04. BOR1; 1c in Brassica napus[J]. BMC Plant Biol,2018,18:193.
[28] Hajiebrahimi A,Owji H,Hemmati S. Genome-wide identification,functional prediction,and evolutionary analysis of the R2R3-MYB superfamily in Brassica napus[J]. Genome,2017,60(10):797-814.
[2] Li W J,Zhang J X,Sun H Y,et al. FveRGA1,encoding a DELLA protein,negatively regulates runner production in Fragaria vesca[J]. Planta,2018,247(4):941-951.
[3]李威,李国瑞,黄凤兰,等. DELLA家族蛋白研究进展[J].安徽农业科学,2016,44(32):147-148.
[4] Zhao X Y,Zhu D F,Zhou B,et al. Over-expression of the At GA2ox8 gene decreases the biomass accumulation and lignification in rapeseed(Brassica napus L.)[J]. J Zhejiang Univ Sci B,2010,11(7):471-481.
[5] Peng J R,Richards D E,Hartley N M,et al.‘Green revolution’ genes encode mutant gibberellin response modulators[J]. Nature,1999,400(6741):256-261.
[6] Pearce S,Saville R,Vaughan S P,et al. Molecular characterization of Rht-1 dwarfing genes in hexaploid wheat[J]. Plant Physiol,2011,157(4):1820-1831.
[7] Chen J H,Cheng T L,Wang P K,et al. Genome-wide bioinformatic analysis of DELLA-family proteins from plants[J]. Plant Omics,2013,6(3):201-207.
[8] Davière J M,Achard P. A pivotal role of DELLAs in regulating multiple hormone signals[J]. Mol Plant,2016,9(1):10-20.
[9] Tyler L. DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis[J].Plant Physiol,2004,135(2):1008-1019.
[10]陈宇杰,刘飞,梁菲菲,等.蓖麻DELLA蛋白家族GAI基因克隆、表达及生物信息学分析[J].内蒙古民族大学学报(自然科学版),2017,32(4):320-327.
[11]张文颖,王晨,朱旭东,等.葡萄全基因组DELLA蛋白基因家族鉴定及其应答外源赤霉素调控葡萄果实发育的特征[J].中国农业科学,2018,51(16):3130-3146.
[12] Gao Y,Chen J M,Zhao Y,et al. Molecular cloning and expression analysis of a RGA-like gene responsive to plant hormones in Brassica napus[J]. Mol Biol Rep,2012,39(2):1957-1962.
[13] Sun T P. Gibberellin-GID1-DELLA:A pivotal regulatory module for plant growth and development[J].Plant Physiol,2010,154(2):567-570.
[14] Murase K,Hirano Y,Sun T P,et al. Gibberellin-induced DELLA recognition by the gibberellin receptor GID1[J]. Nature,2008,456(7221):459-463.
[15] Fu X. Gibberellin-mediated proteasome-dependent degradation of the barley DELLA protein SLN1 repressor[J]. Plant Cell Online,2002,14(12):3191-3200.
[16] Ueguchi-Tanaka M,Nakajima M,Katoh E,et al. Molecular interactions of a soluble gibberellin receptor,GID1,with a rice DELLA protein,SLR1,and gibberellin[J]. Plant Cell Online,2007,19(7):2140-2155.
[17] Zhao B,Li H T,Li J J,et al. Brassica napus DS-3,encoding a DELLA protein,negatively regulates stem elongation through gibberellin signaling pathway[J]. Theor Appl Genet,2017,130(4):727-741.
[18] Li H T,Wang B,Zhang Q H,et al. Genome-wide analysis of the auxin/indoleacetic acid(Aux/IAA)gene family in allotetraploid rapeseed(Brassica napus L.)[J]. BMC Plant Biol,2017,17:204.
[19] Tamura K,Stecher G,Peterson D,et al. MEGA6:molecular evolutionary genetics analysis version 6. 0[J].Mol Biol Evol,2013,30(12):2725-2729.
[20]李晓康,刘红芳,刘婧琳,等.油菜miR156基因家族及其靶基因生物信息学分析及鉴定[J].中国油料作物学报,2018,40(2):163-173.
[21]李春金,郭媛媛,杨启航,等.甘蓝型油菜HMG基因家族的生物信息学分析[J].中国油料作物学报,2018,40(3):318-325.
[22] Wang D P,Wan H L,Zhang S,et al.Γ-MYN:a new algorithm for estimating Ka and Ks with consideration of variable substitution rates[J]. Biol Direct,2009,4(1):20.
[23] Chalhoub B,Denoeud F,Liu S Y,et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J]. Science,2014,345(6199):950-953.
[24] Wu D C,Yao J,Ho K S,et al. Limitations of alignment-free tools in total RNA-seq quantification[J].BMC Genomics,2018,19(1):1-14.
[25]夏胜前,张毅,涂金星.油菜重要性状功能基因研究进展[J].中国油料作物学报,2018,40(5):656-663.
[26] Du H Y,Yang C,Ding G D,et al. Genome-wide identification and characterization of SPX domain-containing members and their responses to phosphate deficiency in Brassica napus[J]. Front Plant Sci,2017,8:35.
[27] Chen H F,Zhang Q,He M L,et al. Molecular characterization of the genome-wide BOR transporter gene family and genetic analysis of Bna C04. BOR1; 1c in Brassica napus[J]. BMC Plant Biol,2018,18:193.
[28] Hajiebrahimi A,Owji H,Hemmati S. Genome-wide identification,functional prediction,and evolutionary analysis of the R2R3-MYB superfamily in Brassica napus[J]. Genome,2017,60(10):797-814.