Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

Nature Communications
Ricardo A Chávez MontesStefan de Folter


Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.


Apr 26, 2000·Proceedings of the National Academy of Sciences of the United States of America·L E GrahamJ S Busse
Dec 18, 2001·Science·K G KarolC F Delwiche
Jul 9, 2002·Genes & Development·Brenda J ReinhartDavid P Bartel
Apr 2, 2004·Nature·Sandra K Floyd, John L Bowman
May 6, 2005·Functional & Integrative Genomics·Anthony A Millar, Peter M Waterhouse
Sep 8, 2005·FEBS Letters·Xuemei Chen
Feb 21, 2006·Genetics·Sandra K FloydJohn L Bowman
Apr 21, 2006·The Plant Journal : for Cell and Molecular Biology·Baohong ZhangTodd A Anderson
Jun 23, 2006·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·John P VogelDevin Coleman-Derr
Sep 16, 2006·Science·Gerald A TuskanDaniel Rokhsar
Aug 28, 2007·Nature·Olivier JaillonFrench-Italian Public Consortium for Grapevine Genome Characterization
Sep 25, 2007·Methods : a Companion to Methods in Enzymology·Cheng LuPamela J Green
Oct 13, 2007·Science·Sabeeha S MerchantArthur R Grossman
Mar 18, 2008·Biochimica Et Biophysica Acta·Michael J Axtell
Jun 19, 2008·Genetics·Martina MrackovaBohuslav Janousek
Jun 21, 2008·RNA·Elena V DolgosheinaPeter J Unrau
Aug 14, 2008·Bioinformatics·Hui Jiang, Wing Hung Wong
Dec 11, 2008·Proceedings of the National Academy of Sciences of the United States of America·Taiowa A MontgomeryJames C Carrington
Jan 17, 2009·Nature Reviews. Genetics·Megha Ghildiyal, Phillip D Zamore
Feb 4, 2009·Nature·Andrew H PatersonDaniel Rokhsar
Feb 26, 2009·Cell·Olivier Voinnet
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Jul 9, 2009·Genome Research·Cameron JohnsonLewis H Bowman
Oct 6, 2009·Methods in Molecular Biology·Monica AccerbiPamela J Green
Oct 6, 2009·Methods in Molecular Biology·Gayathri Mahalingam, Blake C Meyers
Dec 8, 2009·Science·Patrick S SchnableRichard K Wilson
Jan 6, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Sophie JasinskiCharles P Scutt
Feb 12, 2010·Nature·International Brachypodium Initiative
Apr 22, 2010·The Plant Cell·Noah FahlgrenJames C Carrington
Jun 15, 2010·Methods : a Companion to Methods in Enzymology·Michael P RobertsonWilliam G Scott
Jun 18, 2010·Methods : a Companion to Methods in Enzymology·Justin T Low, Kevin M Weeks
Jul 21, 2010·Proceedings of the National Academy of Sciences of the United States of America·Ho-Ming ChenShu-Hsing Wu
Aug 11, 2010·Nature Biotechnology·Ken Garber
Sep 3, 2010·Current Genomics·Christine Lelandais-BrièreCaroline Hartmann
Nov 3, 2010·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Feb 15, 2011·The Plant Cell·Josh T CuperusJames C Carrington
May 11, 2011·Genome Biology·Michael J AxtellEric C Lai
Jul 12, 2011·Nature·Potato Genome Sequencing ConsortiumRichard G F Visser
Oct 15, 2011·Plant Molecular Biology·Matthew W Jones-Rhoades
Nov 24, 2011·Nucleic Acids Research·David M GoodsteinDaniel Rokhsar
Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Pablo A ManavellaDetlef Weigel
May 15, 2012·Nature Biotechnology·Jeffrey L BennetzenKatrien M Devos
Jul 18, 2012·Nature·Angélique D'HontPatrick Wincker
Aug 3, 2012·Frontiers in Plant Science·Moreno ColaiacovoPrimetta Faccioli
Aug 10, 2012·BMC Genomics·Yuanji ZhangGreg Heck
Aug 28, 2012·Methods : a Companion to Methods in Enzymology·Dong-Hoon Jeong, Pamela J Green
Jan 22, 2013·Annual Review of Plant Biology·Michael J Axtell
Oct 29, 2013·Nucleic Acids Research·Paul Julian KerseyDaniel Michael Staines


Oct 10, 2015·Physiologia Plantarum·Alexander KlenovKatalin A Hudak
Apr 12, 2016·Frontiers in Plant Science·Ping WuBin Wang
Jan 6, 2015·The Plant Journal : for Cell and Molecular Biology·Lisa M SmithDetlef Weigel
Apr 22, 2016·Plant Molecular Biology·Anna V ShchennikovaKonstantin G Skryabin
Mar 19, 2015·Frontiers in Plant Science·Flor de Fátima Rosas-CárdenasStefan de Folter
Mar 2, 2016·Genome Biology·Jonathan F WendelRod A Wing
Apr 12, 2016·The Plant Journal : for Cell and Molecular Biology·Stephen DouglassMatteo Pellegrini
Sep 28, 2016·Genome Biology·Chad E NiederhuthRobert J Schmitz
Jan 23, 2016·PloS One·Sarah Jane Rogans, Chrissie Rey
Nov 15, 2017·Bioinformatics·Kuan-Chieh TsengWen-Chi Chang
Nov 8, 2018·Journal of Experimental Botany·Yun-Wei KuoShih-Tong Jeng
Oct 19, 2018·Briefings in Functional Genomics·Kamalakshi DeviPriyabrata Sen
Nov 2, 2016·G3 : Genes - Genomes - Genetics·Daniel Gonzalez-IbeasJill L Wegrzyn
May 20, 2015·BMC Genomics·Jayakumar Belli KullanErica Mica
Jun 25, 2017·Annual Review of Phytopathology·Matthias L BerensKenichi Tsuda
Oct 6, 2017·FEMS Microbiology Reviews·Brice Felden, Luc Paillard
Oct 2, 2019·The Plant Journal : for Cell and Molecular Biology·Lydia GramzowGünter Theißen
Dec 28, 2019·Nucleic Acids Research·José Roberto Bermúdez-BarrientosCei Abreu-Goodger
Dec 14, 2019·Plant, Cell & Environment·Anita Sós-HegedűsGyörgy Szittya
Mar 18, 2020·Genome Research·Alice LunardonMichael J Axtell
Aug 25, 2017·Genome Biology·Chenjiang YouXuemei Chen
Aug 28, 2020·Plant & Cell Physiology·Sha Yu, Jia-Wei Wang
Mar 5, 2016·Mycologia·José Manuel Villalobos-EscobedoNohemí Carreras-Villaseñor
Aug 2, 2019·Plants·Anthony A MillarGigi Wong
Jun 3, 2017·Briefings in Bioinformatics·Alexandre Rossi PaschoalPeter F Stadler
Oct 31, 2018·Scientific Reports·Thaís Cunha de Sousa CardosoMatheus de Souza Gomes
Jun 15, 2019·BMC Genomics·Sridhar RavichandranSylvie Cloutier
Jul 18, 2019·International Journal of Molecular Sciences·Ziwen LiXiangyuan Wan
Feb 7, 2020·Nucleic Acids Research·Anushree NarjalaPadubidri V Shivaprasad
Feb 5, 2016·BMC Plant Biology·Edna Gicela Ortiz MoreaFabio Tebaldi Siveira Nogueira
Jun 9, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Joanna Miskiewicz, Marta Szachniuk
Sep 24, 2018·Functional & Integrative Genomics·Thangasamy SaminathanUmesh K Reddy
Apr 16, 2019·Frontiers in Genetics·José Henrique GaldinoRogerio Margis
Dec 8, 2017·The New Phytologist·Wei-Yi LinTzyy-Jen Chiou
Mar 16, 2017·Plant Cell Reports·Andreia S Rodrigues, Célia M Miguel
Oct 22, 2018·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Mónica Pradillo, Juan L Santos
Aug 21, 2020·G3 : Genes - Genomes - Genetics·Alberto AcquadroSergio Lanteri

Related Concepts

Gene Expression
Small Nuclear RNA
Transcription, Genetic
cDNA Library
RNA Interference

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.