Identification and Expression Analysis of MicroRNA Families Associated with Phase Transition in Chinese Jujube

doi:10.16420/j.issn.0513-353x.2020-0969

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (1): 23-40.doi: 10.16420/j.issn.0513-353x.2020-0969

• Research Papers • Previous Articles Next Articles

Identification and Expression Analysis of MicroRNA Families Associated with Phase Transition in Chinese Jujube

LI Ying¹^,², MENG Xianwei¹^,², MA Zhihang², LIU Mengjun¹^,²^,^**(), ZHAO Jin³^,^**()

¹Research Center of Chinese Jujube,Hebei Agricultural University,Baoding,Hebei 071000,China
²College of Horticulture,Hebei Agricultural University,Baoding,Hebei 071000,China
³College of Life Science,Hebei Agricultural University,Baoding,Hebei 071000,China

Received:2021-04-06 Revised:2021-05-26 Online:2022-01-25 Published:2022-01-24
Contact: LIU Mengjun,ZHAO Jin E-mail:lmj1234567@aliyun.com;zhaojinbd@126.com

Abstract

Abstract:

Current studies have shown that a number of microRNA（miRNA）families are involved in plant flowering time regulation and phase transition,etc. Therefore,it is very instructive for the phase transition regulation of fruit trees to gain insight into microRNA family associated with phase transition in jujube tree. In this study,the new shoots at different development stages（nodes）of jujube progenies were used as materials. Firstly,27 miRNA families with 58 known miRNAs and 23 novel miRNAs were identified by small RNA sequencing analysis in the three different development stages of juvenile,transition and adult period. Among them,44 miRNAs were differentially expressed,including 32 known miRNAs and 12 novel miRNAs. Afterward,six miRNAs（zjmiR156a-5p,zjmiR156j,zjmiR172c,zjmiRmir172e-3p,zjmiRnovel-16 and zjmiRnovel-71）with obviously differential expression in the three development stages were screened out. Their 15 key target genes were also predicted through TargetFinder software,and they are mainly involved in flowering,transcriptional regulation and biosynthesis. Finally,the differential expression of the above-mentioned 12 miRNAs and their 15 key target genes during phase transition were verified by qRT-PCR,and they had positive or negative regulatory relationships. Moreover,the two newly discovered miRNAs（zjmiRnovel-16 and zjmiRnovel-71）may affect the phase transition through photoperiod pathway and glucose metabolism pathway,respectively.

Key words: Ziziphus jujuba, phase transition, microRNA, target gene, small RNA sequencing

CLC Number:

S665.1

LI Ying, MENG Xianwei, MA Zhihang, LIU Mengjun, ZHAO Jin. Identification and Expression Analysis of MicroRNA Families Associated with Phase Transition in Chinese Jujube[J]. Acta Horticulturae Sinica, 2022, 49(1): 23-40.

Figures/Tables 13

References 54

[1]	Allen R S, Li J Y, Stahle M I, Dubroué A, Gubler F, Millar A A. 2007. Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 Family. Proceedings of the National Academy of Sciences of the United States of America, 104 (41):16371-16376.
[2]	Ambros V. 2001. microRNAs:tiny regulators with great potential. Cell, 107 (7):823-826. doi: 10.1016/s0092-8674(01)00616-x pmid: 11779458
[3]	Arya H, Singh M B, Bhalla P L. 2018. Genomic and molecular analysis of conserved and unique features of soybean PIF4. Scientific Reports, 8 (1):12569. doi: 10.1038/s41598-018-30043-2 URL
[4]	Bartel D P. 2004. MicroRNAs:genomics,biogenesis,mechanism,and function. Cell, 116 (2):281-297. doi: 10.1016/s0092-8674(04)00045-5 pmid: 14744438
[5]	Baucher M, Moussawi J, Vandeputte O M, Monteyne D, Mol A, Pérez M D, El J M. 2013. A role for the miR396/GRF network in specification of organ type during flower development,as supported by ectopic expression of Populus trichocarpa miR396c in transgenic tobacco. Plant Biology, 15 (5):892-898. doi: 10.1111/j.1438-8677.2012.00696.x pmid: 23173976
[6]	Bhavani N, Sneha B, Anjan K B. 2017. The essential role of microRNAs in potato tuber development;a mini review. Indian Journal of Plant Physiology, 22 (4):401-410. doi: 10.1007/s40502-017-0324-x URL
[7]	Borges F, Parent J S, van E F, Wolff P, Martínez G, Köhler C, Martienssen R A. 2018. Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis. Nature Genetics, 50 (2):186-192. doi: 10.1038/s41588-017-0032-5 URL
[8]	Chuck G S, Tobias C, Sun Lan, Kraemer F, Li Chenlin, Dibble D, Arora R, Bragg J N, Vogel J P, Singh S, Simmons B A, Pauly M, Hake S. 2011. Overexpression of the maize Corngrass 1 microRNA prevents flowering,improves digestibility,and increases starch content of switchgrass. Proceedings of the National Academy of Sciences of the United States of America, 108 (42):17550-17555.
[9]	Damodharan S, Zhao D Z, Arazi T. 2016. A common miRNA 160-based mechanism regulates ovary patterning,floral organ abscission and lamina outgrowth in tomato. The Plant Journal, 86 (6):458-471. doi: 10.1111/tpj.13127 pmid: 26800988
[10]	Duan Zhongxin. 2012. Expression pattern and functional analysis of microRNA Peu-miR156j and Peu-miR169o from Populus euphratica[M. D. Dissertation]. Beijing: Beijing Forestry University. (in Chinese)
	段中鑫. 2012. 胡杨microRNA Peu-miR156j和Peu-miR169o表达模式分析及功能鉴定[硕士论文]. 北京: 北京林业大学.
[11]	Feng L, Xia R, Liu Y. 2019. Comprehensive characterization of miRNA and PHAS loci in the diploid strawberry(Fragaria vesca)genome. Horticultural Plant Journal, 5 (6):255-267. doi: 10.1016/j.hpj.2019.11.004
[12]	France C, François C, Christine D, Claude W. 2001. A highly specific glucosyltransferase is involved in the synthesis of crocetin glucosylesters in Crocus sativus cultured cells. Journal of Plant Physiology, 158 (5):553-560. doi: 10.1078/0176-1617-00305 URL
[13]	Friedländer M R, Mackowiak S D, Li Na, Chen Wei, Rajewsky N. 2012. miRDeep 2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Research, 40 (1):37-52. doi: 10.1093/nar/gkr688 pmid: 21911355
[14]	Gao Y, Yang F Q, Cao X, Li C M, Wang Y, Zhao Y B, Zeng G J, Chen D M, Han Z H, Zhang X Z. 2014. Differences in gene expression and regulation during ontogenetic phase change in apple seedlings. Plant Molecular Biology Reporter, 32 (2):357-371. doi: 10.1007/s11105-013-0648-2 URL
[15]	Gou Yanli, Zhang Le, Guo Huan, Ma Hongping, Bao Aike. 2020. Research progress on the AP2/ERF transcription factor in plants. Pratacultural Science, 37 (6):1150-1159. (in Chinese)
	苟艳丽, 张乐, 郭欢, 马红萍, 包爱科. 2020. 植物AP2/ERF类转录因子研究进展. 草业科学, 37 (6):1150-1159.
[16]	Gu Jie. 2008. Localization of regulator of G protein signaling(RGS)Protein and its functional analyses in glucose signaling in Arabidopsis thaliana[M. D. Dissertation]. Yangzhou: Yangzhou University. (in Chinese)
	顾杰. 2008. 拟南芥G蛋白信号转导调节蛋白(AtRGS1蛋白)的定位及在葡萄糖信号转导中的功能研究[硕士论文]. 扬州: 扬州大学.
[17]	Hu Z W, Shen X P, Xiang X, Cao J S. 2019. Evolution of MIR159/ 319 genes in Brassica campestris and their function in pollen development. Plant Molecular Biology, 101 (6):537-550. doi: 10.1007/s11103-019-00920-z URL
[18]	Huang Jingmiao. 2018. Prediction and analysis of cis-acting elements and transcription factors of related MdMIR156s during vegetative phase change in apple[M. D. Dissertation]. Beijing: China Agriculture University. (in Chinese)
	黄晶淼. 2018. 苹果阶段转变相关MdMIR156s顺式元件及转录因子预测与分析[硕士论文]. 北京: 中国农业大学.
[19]	José M F Z, Adrián V, Marco T, Isabel M, María I P, Ignacio R S, Antonio L, Detlef W, Juan A G, Javier P A. 2007. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genetics, 39 (8):1033-1037. doi: 10.1038/ng2079 URL
[20]	Ketting R F. 2010. MicroRNA biogenesis and function. An overview. Advances in Experimental Medicine and Biology, 700:1-14. pmid: 21627025
[21]	Kim Wanhui, Ahn H J, Chiou T J, Ahn J H. 2011. The role of the miR399-PHO 2 module in the regulation of flowering time in response to different ambient temperatures in Arabidopsis thaliana. Molecules and Cells, 32 (1):83-88. doi: 10.1007/s10059-011-1043-1 pmid: 21533549
[22]	Kunz H H, Häusler R E, Fettke J, Herbst K, Niewiadomski P, Gierth M, Bell K, Steup M, Flügge U I, Schneider A. 2010. The role of plastidial glucose-6-phosphate/phosphate translocators in vegetative tissues of Arabidopsis thaliana mutants impaired in starch biosynthesis. Plant Biology, 12:115-128. doi: 10.1111/j.1438-8677.2010.00349.x URL
[23]	Li Chenjing, Niu Jianxin, Pei Maosong, Cao Fujun, Quan Shaowen. 2016. Cloning and identification of novel miRNA genes related to calyx persistence in Korla Fragrant Pear. Acta Horticulturae Sinica, 43 (9):1803-1815. (in Chinese)
	李陈静, 牛建新, 裴茂松, 曹福军, 全绍文. 2016. 库尔勒香梨9个新miRNA克隆鉴定. 园艺学报, 43(9):1803-1815.
[24]	Li Zongmei. 2013. Identification and characterization of a novel hydroxycinnamoyl transferase from the Physcomitrella patens and the regulation of P. patens HCT[M. D. Dissertation]. Wuhan;Huazhong Agricultural University. (in Chinese)
	李宗梅. 2013. 小立碗藓羟基肉桂酰酰基转移酶基因功能及调控研究初探[硕士论文]. 武汉: 华中农业大学.
[25]	Liu M J, Wang J R, Wang L L, Liu P, Zhao J, Zhao Z H, Yao S R, Stănică Florin, Liu Z G, Wang L X, Ao C W, Dai L, Li X S, Zhao X, Jia C X. 2020. The historical and current research progress on jujube-a superfruit for the future. Horticulture Research, 7 (1):1683-1698.
[26]	Liu M J, Zhao J, Cai Q L, Liu G C, Wang J R, Zhao Z H, Liu P, Dai L, Yan G J, Wang W J, Li X S, Chen Y, Sun Y D, Liu Z G, Lin M J, Xiao J, Chen Y Y, Li X F, Wu B, Ma Y, Jian J B, Yang W, Yuan Z, Sun X C, Wei Y L, Yu L L, Zhang C, Liao S G, He R J, Guang X M, Wang Z, Zhang Y Y, Luo L H. 2014. The complex jujube genome provides insights into fruit tree biology. Nature Communications, 5 (1):1309-1324.
[27]	Liu Weihua, Lin Yuling, Lin Zhengchun, Ni Shanshan, Lai Zhongxiong. 2018. Analysis of evolution and molecular characteristics of miR172 family members in plants. Chinese Journal of Tropical Crops, 39 (3):525-533. (in Chinese)
	刘炜婳, 林玉玲, 林争春, 倪珊珊, 赖钟雄. 2018. 植物miR172家族成员进化与分子特性分析. 热带作物学报, 39 (3):525-533.
[28]	Luo Hongyu, Yang Jiangwei, Feng Ya, Zhang Huanhuan, Liu Shengyan, Zhang Ning, Si Huaijun. 2021. The effect of Stu-miR156 silencing by STTM technology on potato lateral root development. Acta Horticulturae Sinica, 48 (3):531-538. (in Chinese)
	罗红玉, 杨江伟, 冯亚, 张欢欢, 刘升燕, 张宁, 司怀军. 2021. STTM 技术沉默马铃薯Stu-miR156 对其侧根发育的影响. 园艺学报, 48 (3):531-538.
[29]	Ma J Y, Zhao P, Liu S B, Yang Q, Guo H H. 2020. The Control of developmental phase transitions by microRNAs and their targets in seed plants. International Journal of Molecular Sciences, 21 (6):1971. doi: 10.3390/ijms21061971 URL
[30]	Ma Li, Zhou Li, Xu Hang, Quan Shaowen, Yang Jieping, Niu LJianxini. 2019. Evolutionary characteristics and the expression patterns of miR159 gene family in‘Kuerlexiangli’pear. Journal of Fruit Science, 36 (1):1-10. (in Chinese)
	马丽, 周丽, 徐航, 全绍文, 杨洁萍, 牛建新. 2019. ‘库尔勒香梨’miR159家族成员进化特性及表达分析. 果树学报, 36 (1):1-10.
[31]	Martin R C, Asahina M, Liu Popu, Kristof J R, Coppersmith J L, Pluskota W E, Bassel G W, Goloviznina N A, Nguyen T T, Martínez A C, Arun Kumar M B, Pupel P, Nonogaki H. 2010. The microRNA156 and microRNA 172 gene regulation cascades at post-germinative stages in Arabidopsis. Seed Science Research, 20 (2):79-87. doi: 10.1017/S0960258510000085 URL
[32]	Meng J, Yang J, Peng M D, Liu X L, He H B. 2020a. Genome-wide characterization,evolution,and expression analysis of the Leucine-Rich Repeat Receptor-Like Protein Kinase(LRR-RLK)gene family in Medicago truncatula. Life, 10 (176):176. doi: 10.3390/life10090176 URL
[33]	Meng X W, Li Y, Yuan Y, Zhang Y, Li H T, Zhao J, Liu M J. 2020b. The regulatory pathways of distinct flowering characteristics in Chinese jujube. Horticulture Research, 7 (1):13-19. doi: 10.1038/s41438-019-0236-1 URL
[34]	Mi S J, Cai T, Hu Y G, Chen Y M, Hodges E, Ni F R, Wu L, Li S, Zhou H Y, Long C Z, Chen S, Hannon G J, Qi Y J. 2008. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell, 133 (1):116-127. doi: 10.1016/j.cell.2008.02.034 URL
[35]	Milo J A, Hajime S. 2003. Regulation of flowering time and floral organ identity by a MicroRNA and Its APETALA2-Like target Genes. The Plant Cell, 15:2730-2741 doi: 10.1105/tpc.016238 URL
[36]	Rubenach A J S, Hecht V, Vander Schoor J K, Liew L C, Aubert G, Burstin J, Weller J L. 2017. EARLY FLOWERING 3 redundancy fine-tunes photoperiod sensitivity. Plant Physiology, 173 (4):2253-2264. doi: 10.1104/pp.16.01738 pmid: 28202598
[37]	Schmid M, Uhlenhaut N H, Godard F, Demar M, Bressan R, Weigel D, Lohmann J U. 2003. Dissection of floral induction pathways using global expression analysis. Development, 130 (24):6001-6012. doi: 10.1242/dev.00842 URL
[38]	Shuai Minmin. 2018. Advances of GIGANTEA and CONSTANS,the key genes of flowering in photoperiod pathway[M. D. Dissertation]. Lin’an:Zhejiang A & F University. (in Chinese)
	帅敏敏. 2018. 光周期途径成花关键基因GIGANTEA和CONSTANS的进化机制[硕士论文]. 临安: 浙江农林大学.
[39]	Shuai Minmin, Zhang Qixiang, Huang Youjun. 2019. Evolution of the flowering time gene CONSTANS in a photoperiod pathway. Journal of Zhejiang A & F University, 36 (1):7-13. (in Chinese)
	帅敏敏, 张启香, 黄有军. 2019. 光周期途径成花关键基因CONSTANS的进化机制. 浙江农林大学学报, 36 (1):7-13.
[40]	Spanudakis E, Jackson S. 2014. The role of microRNAs in the control of flowering time. Journal of experimental botany, 65 (2):365-380. doi: 10.1093/jxb/ert453 pmid: 24474808
[41]	Teng Yunlong, Li Chunmin, Zhang Xinzhong, Chen Dongmei, Zeng Guangjuan, Zhao Yongbo, Dong Wenxuan. 2009. SDS-PAGE analysis of phase-transition-related proteins in buds of apple trees. Journal of Fruit Science, 26 (3):375-378. (in Chinese)
	滕云龙, 李春敏, 张新忠, 陈东玫, 曾广娟, 赵永波, 董文轩. 2009. 苹果实生树嫩芽阶段转变相关蛋白质的SDS-PAGE分析. 果树学报, 26 (3):375-378.
[42]	Wang L K, Feng Z X, Wang X, Wang X W, Zhang X G. 2010. DEGseq;an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 26 (1):136-138. doi: 10.1093/bioinformatics/btp612 URL
[43]	Wen M, Shen Y, Shi S H, Tang T. 2012. miREvo;an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments. BMC Bioinformatics 13 (1):140. doi: 10.1186/1471-2105-13-140 URL
[44]	Wu G, Park M Y, Conway S R, Wang J W, Weigel D, Poethig R S. 2009. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell, 138 (4):750-759. doi: 10.1016/j.cell.2009.06.031 URL
[45]	Xu Zihan, Hu Fengrong. 2020. Research progress of miR172 in plant development and regulation. Biotechnology Bulletin, 36 (8):173-184. (in Chinese) doi: 10.13560/j.cnki.biotech.bull.1985.2020-0181
	徐子涵, 胡凤荣. 2020. miR172参与植物发育调控的研究进展. 生物技术通报, 36 (8):173-184. doi: 10.13560/j.cnki.biotech.bull.1985.2020-0181
[46]	Yang L L, Xu M L, Koo Y, He J,Poethig R Scott. 2013. Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156A and MIR156C. eLife, 2:e00260. doi: 10.7554/eLife.00260 URL
[47]	Yu S, Cao L, Zhou C M, Zhang T Q, Lian H, Sun Y, Wu J Q, Huang J R, Wang G D, Wang J W. 2013. Sugar is an endogenous cue for juvenile-to-adult phase transition in plants. eLife, 2:17.
[48]	Yu S, Lian H, Wang J W. 2015. Plant developmental transitions;the role of microRNAs and sugars. Current Opinion in Plant Biology, 27:1-7. doi: 10.1016/j.pbi.2015.05.009 URL
[49]	Zhang C, Xian Z Q, Huang W, Li Z G. 2015. Evidence for the biological function of miR403 in tomato development. Scientia Horticulturae, 197:619-626. doi: 10.1016/j.scienta.2015.10.027 URL
[50]	Zhao Guomiao. 2019. Studies on the miRNA regulation mechanism of heteromorphic leaf development in Populus euphratica[Ph. D. Dissertation]. Beijing: Beijing Forestry University. (in Chinese)
	赵国淼. 2019. 胡杨异形叶发育的miRNA调控机制研究[博士论文]. 北京: 北京林业大学.
[51]	Zhao Hang. 2020. Molecular mechanism of Arabidopsis NF-YA 8 in regulating juvenile-to-adult transition and flowering time[Ph. D. Dissertation]. Tai'an: Shandong Agricultural University. (in Chinese)
	赵航. 2020. 拟南芥NF-YA8调控幼年向成年阶段转型及开花时间的分子机理研究[博士论文]. 泰安: 山东农业大学.
[52]	Zhao Jianguo, Cui Jiawen, Jin Biao. 2015. Research advances of developmental changes of juvenile to adult transition in woody plants. Plant Physiology Journal, 51 (11):1765-1774. (in Chinese)
	赵建国, 崔佳雯, 金飚. 2015. 树木幼年向成年转变的发育调控机制研究进展. 植物生理学报, 51 (11);1765-1774.
[53]	Zheng C F, Ye M X, Sang M G, Wu R L. 2019a. A regulatory network for miR156-SPL module in Arabidopsis thaliana. International Journal of Molecular Sciences, 20 (24):6166. doi: 10.3390/ijms20246166 URL
[54]	Zheng G H, Wei W, Li Y P, Kan L J, Wang F X, Zhang X, Li F, Liu Z C, Kang C Y. 2019b. Conserved and novel roles of miR164-CUC 2 regulatory module in specifying leaf and floral organ morphology in strawberry. New Phytologist, 224 (1):480-492. doi: 10.1111/nph.v224.1 URL

miRNA名称 miRNA name	引物序列（5′-3′） Primer sequence	miRNA名称 miRNA name	引物序列（5′-3′） Primer sequence
zjmiR156a-5p	TGGCTGGGTGACAGAAGAGAGT	zjmiRnovel-16	GGTTAGTGATCCTCCGGAAGATC
zjmiR156j	GGCTGGGTGACAGAAGAGAGA	zjmiRnovel-71	TTGAAGTGTTTGGGGGAACC
zjmiR172c	TGAGAATCTTGATGATGCTGCAG	zjmiRnovel-35	GGCTGCCTCTTGTCTTTCATG
zjmiR172e-3p	TGGAATCTTGATGATGCTGCAT	zjmiRnovel-17	TGCATTTGCACCTGCACCT
zjmiR160a-5p	TGCCTGGCTCCCTGTATGC	zjmiR845a	TCGGCTCTGATACCAATTGATG
zjmiR157a-5p	CGGTTGACAGAAGATAGAGAGCAC	U6	GGGACATCCGATAAAATTG
zjmiR396b-5p	TGGTTCCACAGCTTTCTTGAACTT	U6	CCAATTTTATCGGATGTCC

miRNA名称 miRNA name	引物序列（5′-3′） Primer sequence	miRNA名称 miRNA name	引物序列（5′-3′） Primer sequence
zjmiR156a-5p	TGGCTGGGTGACAGAAGAGAGT	zjmiRnovel-16	GGTTAGTGATCCTCCGGAAGATC
zjmiR156j	GGCTGGGTGACAGAAGAGAGA	zjmiRnovel-71	TTGAAGTGTTTGGGGGAACC
zjmiR172c	TGAGAATCTTGATGATGCTGCAG	zjmiRnovel-35	GGCTGCCTCTTGTCTTTCATG
zjmiR172e-3p	TGGAATCTTGATGATGCTGCAT	zjmiRnovel-17	TGCATTTGCACCTGCACCT
zjmiR160a-5p	TGCCTGGCTCCCTGTATGC	zjmiR845a	TCGGCTCTGATACCAATTGATG
zjmiR157a-5p	CGGTTGACAGAAGATAGAGAGCAC	U6	GGGACATCCGATAAAATTG
zjmiR396b-5p	TGGTTCCACAGCTTTCTTGAACTT	U6	CCAATTTTATCGGATGTCC

miRNA名称 miRNA name	靶基因 Gene	引物名称 Primer	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reversed primer
zjmiR156a-5p	LOC107411088	GE1	TCACTCTAAACGACCCGCAC	GAAGGCACGGAGGATATCGG
	LOC107411586	TC4M	GTCACAGAGCCCGACATTCA	TTCCAGTTGGCAGGGTTGTT
	LOC107420411	GPT2	TTCGTCTGGTGGGTTGTAGC	GAAGGTGCCGAGGATAGCAA
zjmiR156j	LOC107414106	ERF105-like	ACGTCGTCGGAGAGTAAGGA	AGGTGACAAAGGAGGCACAC
zjmiR156j	LOC107425063	SPL	GCAATGCTGACTTGACCGAC	TACGACGCTCATTGTGTCCA
zjmiR172c	LOC107411289	AP2c	AGAGCCTATGATCGAGCTGC	TCCCATTCGAGCTTCCCATC
zjmiR172e-3p	LOC107413613	AP2e	TTAGGTGGGTTCGACACTGC	CCGACGAAGTATCAGCACGA
zjmiRnovel-16	LOC107416596	PIF4-like	TAGCAGGGTGTCCAGCAATG	TCTGATTGCCTCCGCCTTTT
	LOC107416597	PIF4	GAGTCAACGGTCGGGTTCAA	ATTGGTGCCATCCCACTTCC
	LOC107415240	ELF 3	TGCTGAAGGAAGGGATGCTC	ATTGTGCGGTACAACCCTGA
	LOC107420622	CO-LIKE7-like	AGAGGCAAGCGTGTTGAGAT	GAACCGGCCCTTCATACGAG
zjmiRnovel-71	LOC107422007	cro-GT1	GCTACCGTGTTCGGCATCTA	CCATGAACGTGGGAAGGTCA
	LOC107422008	cro-GT2	CGGACCGTTGATTCAGTCCA	GTGGCTTTGGTAACACGCAG
	LOC107418233	NFYA7	AAGCTGGAGTTCCTTTGCCA	CCGCTTTTGCACGAGATTGT
	LOC107412400	RLK1	GCGCAACAAAGTGGAACCTT	GCATTTGTGCACAGGAGAGC

miRNA名称 miRNA name	靶基因 Gene	引物名称 Primer	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reversed primer
zjmiR156a-5p	LOC107411088	GE1	TCACTCTAAACGACCCGCAC	GAAGGCACGGAGGATATCGG
	LOC107411586	TC4M	GTCACAGAGCCCGACATTCA	TTCCAGTTGGCAGGGTTGTT
	LOC107420411	GPT2	TTCGTCTGGTGGGTTGTAGC	GAAGGTGCCGAGGATAGCAA
zjmiR156j	LOC107414106	ERF105-like	ACGTCGTCGGAGAGTAAGGA	AGGTGACAAAGGAGGCACAC
zjmiR156j	LOC107425063	SPL	GCAATGCTGACTTGACCGAC	TACGACGCTCATTGTGTCCA
zjmiR172c	LOC107411289	AP2c	AGAGCCTATGATCGAGCTGC	TCCCATTCGAGCTTCCCATC
zjmiR172e-3p	LOC107413613	AP2e	TTAGGTGGGTTCGACACTGC	CCGACGAAGTATCAGCACGA
zjmiRnovel-16	LOC107416596	PIF4-like	TAGCAGGGTGTCCAGCAATG	TCTGATTGCCTCCGCCTTTT
	LOC107416597	PIF4	GAGTCAACGGTCGGGTTCAA	ATTGGTGCCATCCCACTTCC
	LOC107415240	ELF 3	TGCTGAAGGAAGGGATGCTC	ATTGTGCGGTACAACCCTGA
	LOC107420622	CO-LIKE7-like	AGAGGCAAGCGTGTTGAGAT	GAACCGGCCCTTCATACGAG
zjmiRnovel-71	LOC107422007	cro-GT1	GCTACCGTGTTCGGCATCTA	CCATGAACGTGGGAAGGTCA
	LOC107422008	cro-GT2	CGGACCGTTGATTCAGTCCA	GTGGCTTTGGTAACACGCAG
	LOC107418233	NFYA7	AAGCTGGAGTTCCTTTGCCA	CCGCTTTTGCACGAGATTGT
	LOC107412400	RLK1	GCGCAACAAAGTGGAACCTT	GCATTTGTGCACAGGAGAGC

样本类型 Sample type	童期Juvenile period		过渡期Transition period		成年期Adult period
样本类型 Sample type	种类（%） Category	数量（%） Number	种类（%） category	数量（%） Number	种类（%） category	数量（%） Number
已知miRNA Known miRNA	121（0.03）	22 367（0.33）	152（0.04）	36 906（0.57）	167（0.04）	34 796（0.35）
rRNA	118 138（31.30）	5 535 824（82.23）	112 531（32.56）	5 295 448（81.29）	134 295（28.46）	8 073 860（80.84）
tRNA	4 740（1.26）	181 112（2.69）	4 537（1.31）	152 992（2.35）	5 847（1.24）	340 580（3.41）
snRNA	965（0.26）	4 027（0.06）	1 007（0.29）	4 148（0.06）	1 328（0.28）	7 269（0.07）
snoRNA	576（0.15）	1 674（0.02）	487（0.14）	1 550（0.02）	699（0.15）	2 483（0.02）
重复序列 Repeat	14 323（3.80）	37 164（0.55）	13 090（3.79）	33 685（0.52）	17 230（3.65）	48 302（0.48）
NAT	69 876（18.51）	340 047（5.05）	62 771（18.16）	433 170（6.65）	89 355（18.94）	579 299（5.80）
新miRNA Novel miRNA	61（0.02）	4 221（0.06）	67（0.02）	8 903（0.14）	78（0.02）	9 116（0.09）
exon：+	25 350（6.72）	52 607（0.78）	22 878（6.62）	54 968（0.84）	38 512（8.16）	86 381（0.86）
exon：-	2 263（0.60）	12 125（0.18）	2 841（0.82）	20 279（0.31）	3 489（0.74）	24 477（0.25）
intron：+	6 317（1.67）	48 369（0.72）	5 486（1.59）	34 062（0.52）	8 825（1.87）	79 221（0.79）
intron：-	3 386（0.90）	11 592（0.17）	2 934（0.85）	9 272（0.14）	4 064（0.86）	18 475（0.18）
其他Other	131 297（34.79）	481 402（7.15）	116 873（33.81）	429 158（6.59）	167 937（35.59）	683 147（6.84）
总和Total	377 413	6 732 531	345 654	6 514 541	471 826	9 987 406

Identification and Expression Analysis of MicroRNA Families Associated with Phase Transition in Chinese Jujube

RichHTML

PDF

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 13

References 54

Related Articles 14

Recommended Articles

Metrics

Comments

类型 Sample type	miRNA总数 Total reads	童期 Juvenile period	过渡期 Transition period	成年期 Adult period
已知miRNA前体数 Known miRNA hairpin	58	47	50	55
已知miRNA成熟体数 Known miRNA mature	49	36	40	44
新miRNA前体数 Novel miRNA hairpin	23	22	19	20
新miRNA成熟体数 Novel miRNA mature	17	14	13	15

不同比较组合 Different comparison	差异基因数 Differentially expressed gene number	上调表达 Up regulated	下调表达 Down regulated
童期vs过渡期 Jup vs Trp	27	17	10
童期vs成年期 Jup vs Adp	32	20	12
过渡期vs成年期 Trp vs Adp	25	11	14

miRNA家族 miRNA family	miRNA	成熟体序列（5′-3′） miRNA mature sequence	序列长度/nt Length	靶基因数量 Number
zjMIR156	zjmiR156a-5p	UGACAGAAGAGAGUGAGCAC	20	340
zjMIR156	zjmiR156j	UGACAGAAGAGAGAGAGCAC	20	547
zjMIR157	zjmiR157a-5p	UUGACAGAAGAUAGAGAGCAC	21	121
zjMIR157	zjmiR157d	UGACAGAAGAUAGAGAGCAC	20	265
zjMIR160	zjmiR160a-5p	UGCCUGGCUCCCUGUAUGCCA	21	26
zjMIR164	zjmiR164c-5p	UGGAGAAGCAGGGCACGUGCG	21	93
zjMIR171	zjmiR171a-3p	UGAUUGAGCCGCGCCAAUAUC	21	25
zjMIR171	zjmiR171b-3p	UUGAGCCGUGCCAAUAUCACG	21	29
zjMIR172	zjmiR172a	AGAAUCUUGAUGAUGCUGCAU	21	218
	zjmiR172c	AGAAUCUUGAUGAUGCUGCAG	21	211
	zjmiR172e-3p	GGAAUCUUGAUGAUGCUGCAU	21	205
zjMIR319	zjmiR319a	UUGGACUGAAGGGAGCUCCCU	21	50
zjMIR319	zjmiR319c	UUGGACUGAAGGGAGCUCCUU	21	79
zjMIR390	zjmiR390a-3p	CGCUAUCCAUCCUGAGUUUCA	21	49
zjMIR390	zjmiR390b-3p	CGCUAUCCAUCCUGAGUUCC	20	77
zjMIR396	zjmiR396b-3p	GCUCAAGAAAGCUGUGGGAAA	21	262
zjMIR399	zjmiR399d	UGCCAAAGGAGAUUUGCCCCG	21	53
zjMIRn-16	zjmiRnovel-16	UUAGUGAUCCUCCGGAAGAUC	21	64
zjMIRn-17	zjmiRnovel-17	UGCAUUUGCACCUGCACCUUU	21	104
zjMIRn-34	zjmiRnovel-34	UUGAGCCGUGCCAAUAUCACA	21	54
zjMIRn-35	zjmiRnovel-35	UGGCUGCCUCUUGUCUUUCAUG	22	54
zjMIRn-44	zjmiRnovel-44	UGGAGAAGCAGGGCACAUGCU	21	146
zjMIRn-52	zjmiRnovel-52	UAUAAGUGAUUUGGGCUAGU	20	168
zjMIRn-71	zjmiRnovel-71	UUGAAGUGUUUGGGGGAACCC	21	72

miRNA	靶基因编号 Gene ID	基因命名 Gene name	靶基因注释 Gene description
zjmiR156a-5p	LOC107411088	GE1	1,3-β葡萄糖苷内切酶Glucan endo-1,3-beta-glucosidase
	LOC107411586	TC4M	肉桂酸转移单氧酶Trans-cinnamate 4-monooxygenase
	LOC107420411	GPT2	葡萄糖6-磷酸转运蛋白2 Glucose-6-phosphate/phosphate translocator 2
zjmiR156j	LOC107414106	ERF105-like	乙烯应答元件结合蛋白转录因子 Ethylene-responsive transcription factor ERF105-like
zjmiR156j	LOC107425063	SPL1	鳞片类启动子结合蛋白SPLSquamosa promoter-binding protein 1
zjmiR172c	LOC107411289	AP2c	花同源蛋白 AP2基因Floral homeotic protein APETALA 2
zjmiR172e-3p	LOC107413613	AP2e	花同源蛋白AP2基因Floral homeotic protein APETALA 2
zjmiRnovel-16	LOC107416596	PIF4-like	转录因子PIF4-likeTranscription factor PIF4-like
	LOC107416597	PIF4	转录因子PIF4Transcription factor PIF4
	LOC107415240	CO-LIKE7-like	锌指蛋白类CO-LIKE7-like Zinc finger protein CONSTANS-LIKE 7-like
	LOC107420622	ELF3	早花蛋白3 Protein EARLY FLOWERING 3
zjmiRnovel-71	LOC107422007	cro-GT1	西红花酸葡糖基转移酶Crocetin glucosyltransferase
	LOC107422008	cro-GT2	西红花酸葡糖基转移酶Crocetin glucosyltransferase
	LOC107418233	NFYA7	核转录因子Y亚基A-7-like NFYA7-like Nuclear transcription factor Y subunit A-7-like
	LOC107412400	RLK1	富含亮氨酸重复受体类丝氨酸/苏氨酸蛋白激酶 Probable LRR receptor-like serine/threonine-protein kinase RFK1

[1]	HAN Shuai, WU Jie, ZHANG Heqing, XI Yadong. Identification and Sequence Analysis of Tomato Spotted Wilt Orthotospovirus Infecting Lettuce in Sichuan [J]. Acta Horticulturae Sinica, 2022, 49(9): 2007-2016.
[2]	LIANG Qin, ZHANG Yanhui, KANG Kaiquan, LIU Jinhang, LI Liang, FENG Yu, WANG Chao, YANG Chao, LI Yongyu. Molecular Evolution of MiR168 Family and Their Expression Profiling During Dormancy of Pyrus pyrifolia [J]. Acta Horticulturae Sinica, 2022, 49(5): 958-972.
[3]	GAO Weilin, ZHANG Liman, XUE Chaoling, ZHANG Yao, LIU Mengjun, ZHAO Jin. Expression of E-type MADS-box Genes in Flower and Fruits and Protein Interaction Analysis in Chinese Jujube [J]. Acta Horticulturae Sinica, 2022, 49(4): 739-748.
[4]	GUO Xuemin, WANG Xinrui, WANG Yingying, LI Zheng, MIAO Ningning, WANG Zhaojun. Anatomical Observation on the Tortuousness of Ziziphus jujuba var. tortuosa Branches [J]. Acta Horticulturae Sinica, 2021, 48(9): 1653-1664.
[5]	XIN Haiqing, ZHOU Junyong, SUN Yaoxing, MU Wenlei, YANG Jian, MA Fuli, SUN Jun, XUE Zhengrong, LU Lijuan, SUN Qibao. Differences in the Pericarp Structure and the Expression of Expansin Genes After Irrigation Between Easily Cracked and Resistant Jujube [J]. Acta Horticulturae Sinica, 2021, 48(9): 1785-1793.
[6]	ZHANG Xiaoyi, HONG Yuhui, ZHANG Yuanyuan, LUAN Yushi. Preliminary Study on the Role of sly-miR166b and Its Target Genes in Tomato Resistance to Late Blight [J]. Acta Horticulturae Sinica, 2021, 48(8): 1595-1604.
[7]	LI Linlin1，JIN Hua1，LIU Sichao3，ZOU Jixiang1，and LI Tianlai2,*. Expressied Analysis of miRNA with Tomato JA Deficient Mutant Reponse to Botrytis cinerea Infection [J]. ACTA HORTICULTURAE SINICA, 2020, 47(7): 1323-1334.
[8]	QIU Xiaojun, TAN Qunyun, XIAO Qingming, MEI Shiyong, and ZHANG Jifang. Pathogen Identification of Virus Disease and Evaluation for Germplasm Disease Resistance in Radish [J]. Acta Horticulturae Sinica, 2020, 47(10): 1947-1955.
[9]	ZHU Zaobing，YU Xiaqing，ZHAI Yufei，WANG Panqiao，ZHAO Qinzheng，LI Ji，LOU Qunfeng，and CHEN Jinfeng. Cloning and Functional Analysis of microRNA171 in Cucumber [J]. ACTA HORTICULTURAE SINICA, 2019, 46(5): 864-876.
[10]	ZHANG Yanping1,2,*，LIU Zhaokun3，ZHU Xudong4，WANG Chen4，LI Qingkui1，YUAN Weiming1，and LOU Xiaoming1. Identification of miR160a and Its Target Gene ARFs in Peach Fruit and the Response Analysis of IAA [J]. ACTA HORTICULTURAE SINICA, 2019, 46(4): 613-622.
[11]	MA Xinrui，LI Liang，LIU Jinhang，YANG Mengjie，CHEN Jie，LIANG Qin，WU Shaohua，and LI Yongyu. Identification and Differentially Expressed Analysis of microRNA Associated with Dormancy of Pear Flower Buds [J]. ACTA HORTICULTURAE SINICA, 2018, 45(11): 2089-2105.
[12]	XU Yuanyuan1，ZHU Shiping1，LIU Xiaona1，LI Qingping2，and ZHAO Xiaochun1,*. Effects of Grafting on MicroRNAs Expression in Citrus [J]. ACTA HORTICULTURAE SINICA, 2017, 44(7): 1263-1274.
[13]	YAN Ming-Ke, XU Qiang, LIU Chun-Yan, ZHANG Qiong, YAO Xiao-Hong. Preliminary Investigation on Sex Differentiation of Actinidia chinensis by High-throughput microRNAs Sequencing [J]. ACTA HORTICULTURAE SINICA, 2015, 42(7): 1260-1272.
[14]	SONG Chang-nian;JIA Qi-dong;WANG Chen;LI Fei;ZHANG Zhen;and FANG Jing-gui;. Computational Identification and Analysis of the Putative microRNAs in 32 Fruit Crops [J]. ACTA HORTICULTURAE SINICA, 2010, 37(6): 869-879.