|本期目录/Table of Contents|

[1]蒋梦琦,苏立遥,黄倏祺,等.龙眼miR156家族及其调控靶标SPL的生物信息学和表达模式[J].应用与环境生物学报,2020,26(03):558-565.[doi:10.19675/j.cnki.1006-687x.2019.07024]
 JIANG Mengqi,SU Liyao,HUANG Shuqi,et al.Bioinformatics and expression pattern analysis of miR156 family and its regulatory target SPL in Dimocarpus longan[J].Chinese Journal of Applied & Environmental Biology,2020,26(03):558-565.[doi:10.19675/j.cnki.1006-687x.2019.07024]
点击复制

龙眼miR156家族及其调控靶标SPL的生物信息学和表达模式()
分享到:

《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
26卷
期数:
2020年03期
页码:
558-565
栏目:
研究论文
出版日期:
2020-06-25

文章信息/Info

Title:
Bioinformatics and expression pattern analysis of miR156 family and its regulatory target SPL in Dimocarpus longan
作者:
蒋梦琦苏立遥黄倏祺陈旭徐小萍张梓浩赖钟雄林玉玲
福建农林大学园艺植物生物工程研究所 福州 350002
Author(s):
JIANG Mengqi SU Liyao HUANG Shuqi CHEN Xu XU Xiaoping ZHANG Zihao LAI Zhongxiong & LIN Yuling?
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
关键词:
龙眼miR156进化特性体胚发生SPL
Keywords:
Dimocarpus longan miR156 evolutionary characteristics somatic embryogenesis SPL
DOI:
10.19675/j.cnki.1006-687x.2019.07024
摘要:
为了解miR156基因家族的进化特性及其在龙眼早期体胚发生过程中的调控作用,对植物miR156家族成员的成熟体和前体序列进行多重比对和进化特性分析,并对龙眼miR156基因家族成员进行了前体(pre-miRNA)二级结构预测、靶基因预测及裂解位点验证,利用qPCR技术探究龙眼体胚发生早期miR156a与靶基因SPL6/9/16调控模式. 结果表明,龙眼miR156家族含有13条成熟体序列和6条前体序列. Mfold预测显示,pre-miR156家族6个成员的序列均能形成典型稳定的茎环二级结构,它们的最小折叠自由能(ΔG)在-43.30--62.60 kal/mol;成熟序列的碱基保守性高. 系统发育进化树分析显示,龙眼miR156家族与水稻、拟南芥的miR156亲缘关系更为接近. 靶基因预测显示,龙眼miR156a的靶基因是SPL2、SPL6、SPL9、SPL16、SPL18;利用改良的RLM-RACE在龙眼愈伤组织中检测到SPL6/9/16的断裂片段,miR156a在与靶基因mRNA互补的第10个核苷酸处切割靶标mRNA. 实时荧光定量PCR显示,在龙眼体胚发生早期miR156a在0-9 d表达平稳,仅在球形胚(globular embryos,GE)阶段显著下调,SPL6/9/16表达量持续上调,在GE阶段表达量最高,提示SPL6/9/16的大量积累对龙眼球形胚形态建成具有重要作用. 本研究表明植物miR156基因家族成熟体序列高度保守,且miR156a的下调表达与靶基因SPL6/9/16的大量积累可能对龙眼球形胚的建成具有重要意义. (图7 表2 参22)
Abstract:
The miR156 gene family is one of the most ancient and conserved families involved in the regulation of plant growth and development. However, the evolutionary characteristics of miR156 gene family and its function in Dimocarpus longan somatic embryos have not been reported yet. Therefore, we investigated the evolutionary characteristics of miR156 gene family and its regulatory role in the early somatic embryogenesis of longan. We analyzed the mature and precursor sequences and performed the phylogenetic analysis of longon with other plants. We also predicted the secondary structure of precursors miR156 (pre-miR156) family members and analyzed the regulatory patterns of miR156a and its target genes SPL6/9/16 during the early somatic embryogenesis of longan. The longan miR156 family comprised 13 mature sequences and 6 precursor sequences. Mfold prediction analysis revealed that the sequences of pre-miR156 family members could form typical stable secondary stem-loop structures, and their minimum folding free energy (ΔG) ranged from -43.30 kal/mol to -62.60 kal/mol. Multiple sequence alignment of these pre-miR156 members showed that the regions generating the mature miRNA were highly conserved. Phylogenetic tree analysis showed that miR156 family of longan was more closely related to those from rice and Arabidopsis thaliana. Based on the target gene prediction analysis, the target genes of miR156a were found to be SPL2, SPL6, SPL9, SPL16, and SPL18. We detected fragments of SPL6, SPL9, and SPL16 in longan callus using an improved RLM-RACE method, and miR156a was found to cleave the target mRNA at the 10th nucleotide. Fluorescence based quantitative real-time PCR (qRT-PCR) revealed that in the early somatic embryos of longan, the expression of miR156a was stable at days 0-9, but decreased significantly in globular embryos (GE), while the expression levels of SPL6, SPL9, and SPL16 increased significantly. These results indicate that the mature sequences of miR156 families in plants are highly conserved, and the decrease in miR156 and accumulation of SPL6, SPL9, and SPL16 might be significant for the formation of longan globular embryos.

参考文献/References:

1 Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 [J]. Cell, 1993, 75 (5): 843
2 Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of Plant MicroRNA Targets [J]. Cell, 2002, 110 (4): 513-520
3 Wang J W, Czech B, Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana [J]. Cell, 2009, 138 (4): 738-749
4 Schwarz S, Grande AV, Bujdoso N, Saedler H, Huijser P. The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis [J]. Plant Mol Biol, 2008, 67 (1-2): 183
5 Yu N, Niu Q W, Ng KH, Ng KH, Chua NH. The role of miR156/SPLs modules in Arabidopsis lateral root development [J]. Plant J, 2015, 83 (4): 673-685
6 Gou JY, Felippes FF, Liu CJ, Liu CJ, Weigel D, Wang JW. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor [J]. Plant Cell, 2011, 23 (4): 1512-1522
7 Luo Y C, Zhou H, Li Y, Chen JY,Yang JH, Chen YQ, Qu LH. Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development [J]. FEBS Lett, 2006, 580 (21): 5111-5116
8 张俊红, 张守攻, 吴涛, 韩素英, 杨文华, 齐力旺. 落叶松体胚发育中5个miRNA前体与成熟体的表达[J]. 植物学报, 2012, 47 (5): 462-473 [Zhang JH, Zhang SG, Wu T, Han SY, Yang WH, Qi LW. Expression of five miRNA precursors and mature bodies in larch embryo development [J]. Plant J, 2012, 47 (5): 462-473]
9 Liu MY, Wu XM, Long JM, Guo WW. Genomic characterization of miR156 and SQUAMOSA promoter binding protein-like genes in sweet orange (Citrus sinensis) [J]. Plant Cell Tissue Organ Cult, 2017, 130 (1): 1-14
10 Wang SK, Wu K, Yuan QB,Liu XY, Liu ZB, Lin XY, Zeng RZ, Zhu HT, Dong GJ, Qian Q, Zhang GQ, Fu XD. Control of grain size, shape and quality by OsSPL16 in rice [J]. Nat Genet, 2012, 44 (8): 950-954
11 Cui LG, Shan JX, Shi M, Gao JP, Lin HX. The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants [J]. Plant J, 2015, 80 (6): 1108-1117
12 Ge YF, Han JY, Zhou GX, Xu YM, Ding Y, Shi M, Guo CK, Wu G. Silencing of miR156 confers enhanced resistance to brown planthopper in rice [J]. Planta, 2018, 248 (4): 813-826
13 Lin YL, Min JM, Lai RL, Wu ZY, Chen YK, Yu LL, Cheng CZ, Jin YC, Tian QL1, Liu QF, Liu WH, Zhang CG, Lin LX, Hu Y, Zhang DM, Thu M, Zhang ZH, Liu SC, Zhong CS, Fang XD, Wang J, Yang HM, Varshney K, Yin Y, Lai ZX. Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics [J]. Gigascience, 2017, 6 (5): 1-14
14 Lin YL, Lai ZX. Comparative analysis reveals dynamic changes in miRNAS and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour.) [J]. PLoS ONE, 2013, 8 (4): e60337
15 曾友竞. miPEPs在龙眼体胚发生过程中的应用研究[D]. 福州: 福建农林大学, 2017 [Zeng YJ. Application of miPEPs in somatic embryogenesis of Dimocarpus longan Lour. [D]. Fuzhou: Fujian Agriculture and Forestry University, 2017]
16 Lin YL, Lai ZX. Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree [J]. Plant Sci, 2010, 178 (4): 359-365
17 李晓康, 刘红芳, 刘婧琳, 郑明, 华玮. 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): 4-14 [Li XK, Liu HF, Liu JL, Zheng M, Hua W. Identification and bioinformatics of bna-miR156 gene family and target genes in rapeseed (Brassica napus L.) [J]. Chin J Oil Crop Sci, 2018, 40 (2): 4-14]
18 Nodine MD, Bartel DP. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis [J]. Genes Dev, 2010, 24 (23): 2678-2692
19 Chávez-Hernández EC, D. Alejandri-Ramírez N, Juárez-González VT, D. Dinkova T. Maize miRNA and target regulation in response to hormone depletion and light exposure during somatic embryogenesis [J]. For Plant Sci, 2015, 6: 555
20 Wu XM, Kou SJ, Liu YL, Fang YN, Xu Q, Guo WW. Genomewide analysis of small RNAs in nonembryogenic and embryogenic tissues of citrus: microRNA- and siRNA-mediated transcript cleavage involved in somatic embryogenesis [J]. Plant Biol J, 2015, 13 (3): 383-394
21 Long JM, Liu CY, Feng MQ, Liu Y, Wu XM, Guo WW. Corrigendum: miR156-SPL modules regulate induction of somatic embryogenesis in citrus callus [J]. J Exp Bot, 2018, 69 (12): 2979-2993
22 Zhang TQ, Lian H, Tang HB, Dolezal K, Zhou CM, Yu S, Chen JH, Chen Q, Liu HT, Ljung K, Wang JW. An intrinsic microRNA timer regulates progressive decline in shoot regenerative capacity in plants [J]. Plant Cell, 2015, 27 (2): 349-360

相似文献/References:

[1]邱栋梁,刘星辉,王湘平.模拟酸雨对龙眼叶绿体的伤害效应[J].应用与环境生物学报,2002,8(02):154.
 QIU Dongliang,et al..Injury effects of simulated acid rain on chloroplasts of longan leaves[J].Chinese Journal of Applied & Environmental Biology,2002,8(03):154.
[2]邱栋梁,刘星辉,郭素枝.模拟酸雨对龙眼幼果纤维素酶活性和内源激素含量的影响[J].应用与环境生物学报,2004,10(01):35.
 QIU Dongliang,et al..Effects of simulated acid rain on cellulase activity and contents of endogenous hormone in young fruit of longan[J].Chinese Journal of Applied & Environmental Biology,2004,10(03):35.
[3]林玉玲,赖钟雄.龙眼胚性愈伤组织Cu/Zn-SOD分子伴侣基因CCS的克隆及其在体胚发生过程中的表达分析[J].应用与环境生物学报,2012,18(03):351.[doi:10.3724/SP.J.1145.2012.00351]
 LIN Yuling,LAI Zhongxiong.Cloning of Copper Chaperone for Superoxide Dismutase Gene CCS from Embryogenic Callus of Dimocarpus longan Lour. and Its Expression Analysis During Somatic Embryogenesis[J].Chinese Journal of Applied & Environmental Biology,2012,18(03):351.[doi:10.3724/SP.J.1145.2012.00351]
[4]赖瑞联,林玉玲,赖钟雄.龙眼生长素受体基因TIR1的克隆及其与miR393互作关系[J].应用与环境生物学报,2016,22(01):95.[doi:10.3724/SP.J.1145.2015.05051]
 LAI Ruilian,LIN Yuling & LAI Zhongxiong**.Cloning of auxin receptor gene TIR1 and its interaction with miR393 in Dimocarpus longan Lour.[J].Chinese Journal of Applied & Environmental Biology,2016,22(03):95.[doi:10.3724/SP.J.1145.2015.05051]
[5]陈旭,曾友竞,王嘉毅,等.龙眼miR159家族成员进化特性及时空表达[J].应用与环境生物学报,2017,23(04):602.[doi:10.3724/SP.J.1145.2017.03011]
 CHEN Xu,ZENG Youjing,WANG Jiayi,et al.Effect of main grain components on the starch swelling power of Tibetan hull-less barley (Hordeum vulgare var. nudum)[J].Chinese Journal of Applied & Environmental Biology,2017,23(03):602.[doi:10.3724/SP.J.1145.2017.03011]
[6]王云,彭丽云,孙雪丽,等.龙眼Hsf基因家族全基因组鉴定及体胚发生过程中的表达分析[J].应用与环境生物学报,2019,25(02):420.[doi:10.19675/j.cnki.1006-687x.2018.06004]
 WANG Yun,PENG Liyun,SUN Xueli,et al.Genome-wide identification of longan Hsf family members and their functional analysis during somatic embryogenesis in longan[J].Chinese Journal of Applied & Environmental Biology,2019,25(03):420.[doi:10.19675/j.cnki.1006-687x.2018.06004]
[7]苏立遥,黄倏祺,蒋梦琦,等.龙眼miR403及其候选靶标对外源激素的响应模式以及在龙眼体胚中的表达模式[J].应用与环境生物学报,2019,25(04):977.[doi:10.19675/j.cnki.1006-687x.2019.03058]
 SU Liyao,HUANG Shuqi,JIANG Mengqi,et al.The response patterns of miR403 and its candidate targets to exogenous hormones and their expression profiles in the longan somatic embryo[J].Chinese Journal of Applied & Environmental Biology,2019,25(03):977.[doi:10.19675/j.cnki.1006-687x.2019.03058]
[8]李汉生,孙刚,陈晓慧,等.龙眼BRI1基因家族的全基因组鉴定及光照响应表达[J].应用与环境生物学报,2020,26(01):125.[doi:10.19675/j.cnki.1006-687x.2019.07053]
 LI Hansheng,SUN Gang,CHEN Xiaohui,et al.Genome-wide identification and response light expression analysis of the BRI1 family in Dimocarpus longan Lour[J].Chinese Journal of Applied & Environmental Biology,2020,26(03):125.[doi:10.19675/j.cnki.1006-687x.2019.07053]
[9]刘蒲东,张舒婷,陈晓慧,等.龙眼GRF家族全基因组鉴定及表达模式[J].应用与环境生物学报,2020,26(02):236.[doi:10.19675/j.cnki.1006-687x.2019.06028]
 LIU Pudong,ZHANG Shuting,CHEN Xiaohui,et al.Genomic identification and expression patterns of the longan GRF family[J].Chinese Journal of Applied & Environmental Biology,2020,26(03):236.[doi:10.19675/j.cnki.1006-687x.2019.06028]
[10]廖斌,徐小萍,李珊珊,等.苯丙氨酸和茉莉酸甲酯对龙眼胚性悬浮细胞柯里拉京积累的影响[J].应用与环境生物学报,2020,26(02):287.[doi:10.19675/j.cnki.1006-687x.2019.06001]
 LIAO Bin,XU Xiaoping,LI Shanshan,et al.Effects of phenylalanine and methyl jasmonate on the growth and corilagin accumulation of embryogenic suspension cells in Dimocarpus longan Lour.[J].Chinese Journal of Applied & Environmental Biology,2020,26(03):287.[doi:10.19675/j.cnki.1006-687x.2019.06001]

更新日期/Last Update: 2020-06-25