Identification of miRNAs and Their Target Genes in Taraxacum spp

被引:0
作者
Karimi, A. A. [1 ]
Naghavi, M. R. [1 ]
Peighambari, S. A. [1 ]
Sobhani, A. [2 ]
Rasoulnia, A. [1 ]
机构
[1] Univ Tehran, Coll Agr & Nat Resources, Dept Agron & Plant Breeding, Div Biotechnol, POB 31587-11167, Karaj, Iran
[2] Agr Res Educ & Extens Org AREEO, Isfahan Branch, Agr Biotechnol Res Inst Iran, POB 85135-487, Esfahan, Iran
来源
JOURNAL OF AGRICULTURAL SCIENCE AND TECHNOLOGY | 2022年 / 24卷 / 06期
基金
美国国家科学基金会;
关键词
MicroRNA; Natural rubber; RNA-seq; Taraxacum kok-saghyz; Terpene; NATURAL-RUBBER; MICRORNAS; TOOL;
D O I
暂无
中图分类号
S [农业科学];
学科分类号
09 ;
摘要
MicroRNAs are endogenous noncoding RNA that play vital roles in all plant cellular metabolic processes by mediating target gene expression. To date, miRNAs in Taraxacum spp., which is an important industrial plant, have remained largely unknown. In the present study, 970 miRNAs from 399 families were identified in Taraxacum spp by conducting computational approaches. The most frequent miRNAs in Taraxacum spp was miR5021. According to the KEGG results, miR5021, miR838, and miR1533 are related to the terpene biosynthesis pathway, while miR5015b, and miR1436 are involved in the starch and sucrose biosynthesis pathways. Quantitative real-time PCR assay was performed to validate the expression levels of five predicted miRNAs and 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase (HMGCR) and invertase as the target genes. Results indicated that the highest relative expression of miR1533 and miR1436 occurred in the flower, while the highest transcripts levels of miR5015b were observed in the stem. In addition, the higher relative expression level of the miR5021 and miR838 was consistent with the lower expression level of the HMGCR gene in all tissue, suggesting that miR5021 and miR838 are involved in regulating HMGCR gene expression. Since mevalonate pathway is the main source of isopentenyl pyrophosphate, which is used in the synthesis of rubber, miR5021 and miR838 play an important role in the production of rubber by regulating the expression of HMGCR enzyme. These findings will accelerate future perspective studies on the regulatory mechanisms of miRNAs in Taraxacum koksaghyz.
引用
收藏
页码:1457 / 1471
页数:15
相关论文
共 50 条
[1]   Despacito: the slow evolutionary changes in plant microRNAs [J].
Baldrich, Patricia ;
Beric, Aleksandra ;
Meyers, Blake C. .
CURRENT OPINION IN PLANT BIOLOGY, 2018, 42 :16-22
[2]   Trimmomatic: a flexible trimmer for Illumina sequence data [J].
Bolger, Anthony M. ;
Lohse, Marc ;
Usadel, Bjoern .
BIOINFORMATICS, 2014, 30 (15) :2114-2120
[3]   Real-time quantification of microRNAs by stem-loop RT-PCR [J].
Chen, CF ;
Ridzon, DA ;
Broomer, AJ ;
Zhou, ZH ;
Lee, DH ;
Nguyen, JT ;
Barbisin, M ;
Xu, NL ;
Mahuvakar, VR ;
Andersen, MR ;
Lao, KQ ;
Livak, KJ ;
Guegler, KJ .
NUCLEIC ACIDS RESEARCH, 2005, 33 (20) :e179.1-e179.9
[4]   Blast2GO:: a universal tool for annotation, visualization and analysis in functional genomics research [J].
Conesa, A ;
Götz, S ;
García-Gómez, JM ;
Terol, J ;
Talón, M ;
Robles, M .
BIOINFORMATICS, 2005, 21 (18) :3674-3676
[5]   psRNATarget: a plant small RNA target analysis server [J].
Dai, Xinbin ;
Zhao, Patrick Xuechun .
NUCLEIC ACIDS RESEARCH, 2011, 39 :W155-W159
[6]   Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data [J].
Duan, Jialei ;
Xia, Chuan ;
Zhao, Guangyao ;
Jia, Jizeng ;
Kong, Xiuying .
BMC GENOMICS, 2012, 13
[7]   Differential microRNA Analysis of Glandular Trichomes and Young Leaves in Xanthium strumarium L. Reveals Their Putative Roles in Regulating Terpenoid Biosynthesis [J].
Fan, Rongyan ;
Li, Yuanjun ;
Li, Changfu ;
Zhang, Yansheng .
PLOS ONE, 2015, 10 (09)
[8]   Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum) [J].
Frazier, Taylor P. ;
Xie, Fuliang ;
Freistaedter, Andrew ;
Burklew, Caitlin E. ;
Zhang, Baohong .
PLANTA, 2010, 232 (06) :1289-1308
[9]   De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis [J].
Haas, Brian J. ;
Papanicolaou, Alexie ;
Yassour, Moran ;
Grabherr, Manfred ;
Blood, Philip D. ;
Bowden, Joshua ;
Couger, Matthew Brian ;
Eccles, David ;
Li, Bo ;
Lieber, Matthias ;
MacManes, Matthew D. ;
Ott, Michael ;
Orvis, Joshua ;
Pochet, Nathalie ;
Strozzi, Francesco ;
Weeks, Nathan ;
Westerman, Rick ;
William, Thomas ;
Dewey, Colin N. ;
Henschel, Robert ;
Leduc, Richard D. ;
Friedman, Nir ;
Regev, Aviv .
NATURE PROTOCOLS, 2013, 8 (08) :1494-1512
[10]   An overview of microRNAs [J].
Hammond, Scott M. .
ADVANCED DRUG DELIVERY REVIEWS, 2015, 87 :3-14