Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

被引：87

作者：

Zhang, Runxuan ^{[1
]}

Marshall, David ^{[1
]}

Bryan, Glenn J. ^{[1
]}

Hornyik, Csaba ^{[1
]}

机构：

[1] James Hutton Inst, Dundee, Scotland

来源：

PLOS ONE | 2013年 / 8卷 / 02期

基金：

英国生物技术与生命科学研究理事会;

关键词：

PLANT SMALL RNAS; STRESS RESPONSES; SIRNA BIOGENESIS; GENOME SEQUENCE; MICRORNAS; GENES; ARABIDOPSIS; EVOLUTION; ROLES; EXPRESSION;

D O I：

10.1371/journal.pone.0057233

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Micro RNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. While the diverse functions of miRNAs in model plants have been well studied, the impact of miRNAs in crop plant biology is poorly understood. Here we used high-throughput sequencing and bioinformatics analysis to analyze miRNAs in the tuber bearing crop potato (Solanum tuberosum). Small RNAs were analysed from leaf and stolon tissues. 28 conserved miRNA families were found and potato-specific miRNAs were identified and validated by RNA gel blot hybridization. The size, origin and predicted targets of conserved and potato specific miRNAs are described. The large number of miRNAs and complex population of small RNAs in potato suggest important roles for these non-coding RNAs in diverse physiological and metabolic pathways.

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页数：9

相关论文

共 54 条

[1] From the model to the crop: genes controlling tuber formation in potato [J].

Abelenda, Jose A. ;

Navarro, Cristina ;

Prat, Salome .

CURRENT OPINION IN BIOTECHNOLOGY, 2011, 22 (02) :287-292

[2] Variations on RNA folding and alignment:: lessons from Benasque [J].

Bompfuenewerer, Athanasius F. ;

Backofen, Rolf ;

Bernhart, Stephan H. ;

Hertel, Jana ;

Hofacker, Ivo L. ;

Stadler, Peter F. ;

Will, Sebastian .

JOURNAL OF MATHEMATICAL BIOLOGY, 2008, 56 (1-2) :129-144

[3] 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants [J].

Chen, Ho-Ming ;

Chen, Li-Teh ;

Patel, Kanu ;

Li, Yi-Hang ;

Baulcombe, David C. ;

Wu, Shu-Hsing .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (34) :15269-15274

[4]

Chen X, 2012, CURR OPIN GENET DEV

[5] Small RNAs and Their Roles in Plant Development [J].

Chen, Xuemei .

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, 2009, 25 :21-44

[6] Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis [J].

Cuperus, Josh T. ;

Carbonell, Alberto ;

Fahlgren, Noah ;

Garcia-Ruiz, Hernan ;

Burke, Russell T. ;

Takeda, Atsushi ;

Sullivan, Christopher M. ;

Gilbert, Sunny D. ;

Montgomery, Taiowa A. ;

Carrington, James C. .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2010, 17 (08) :997-U111

[7] psRNATarget: a plant small RNA target analysis server [J].

Dai, Xinbin ;

Zhao, Patrick Xuechun .

NUCLEIC ACIDS RESEARCH, 2011, 39 :W155-W159

[8] Roles for MicroRNAs in Conferring Robustness to Biological Processes [J].

Ebert, Margaret S. ;

Sharp, Phillip A. .

CELL, 2012, 149 (03) :515-524

[9] High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes [J].

Fahlgren, Noah ;

Howell, Miya D. ;

Kasschau, Kristin D. ;

Chapman, Elisabeth J. ;

Sullivan, Christopher M. ;

Cumbie, Jason S. ;

Givan, Scott A. ;

Law, Theresa F. ;

Grant, Sarah R. ;

Dangl, Jeffery L. ;

Carrington, James C. .

PLOS ONE, 2007, 2 (02)

[10] Discovering microRNAs from deep sequencing data using miRDeep [J].

Friedlaender, Marc R. ;

Chen, Wei ;

Adamidi, Catherine ;

Maaskola, Jonas ;

Einspanier, Ralf ;

Knespel, Signe ;

Rajewsky, Nikolaus .

NATURE BIOTECHNOLOGY, 2008, 26 (04) :407-415

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