A genome-wide characterization of microRNA genes in maize.

PLoS Genetics
Lifang ZhangDoreen Ware

Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of an...Continue Reading

References

Oct 25, 1990·Nucleic Acids Research·T D Schneider, R M Stephens
Jan 1, 1970·Molecular & General Genetics : MGG·R CuninN Glansdorff
Sep 14, 2000·Genome Research·W B BarbazukS L Johnson
Jun 24, 1997·Proceedings of the National Academy of Sciences of the United States of America·B S Gaut, J F Doebley
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Jul 9, 2002·Genes & Development·Brenda J ReinhartDavid P Bartel
Jul 18, 2002·The Plant Cell·Cesar LlaveJames C Carrington
Feb 13, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·J. SchlossS. Kresovich
May 3, 2003·Current Biology : CB·Zhixin XieJames C Carrington
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Sep 17, 2003·The Plant Journal : for Cell and Molecular Biology·Jeong Hoe KimHans Kende
Nov 25, 2003·Science·Michael Lynch, John S Conery
Dec 20, 2003·Science·Lance E PalmerW Richard McCombie
Dec 20, 2003·Science·C A WhitelawJ Quackenbush
Mar 6, 2004·Nature·Catherine A Kidner, Robert A Martienssen
Mar 17, 2004·Genetics·Richard J LanghamMichael Freeling
Mar 17, 2004·Nucleic Acids Research·Jia-Fu WangLiang-Hu Qu
Apr 30, 2004·European Journal of Clinical Nutrition·P C ElwoodA R Ness
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Jun 18, 2004·Molecular Cell·Matthew W Jones-Rhoades, David P Bartel
Jul 13, 2004·Bioinformatics·Brian J HaasSteven L Salzberg
Jul 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Eric BonnetYves Van de Peer
Sep 3, 2004·Development·Michelle T JuarezMarja C P Timmermans
Sep 15, 2004·Trends in Genetics : TIG·Cathal Seoighe, Chris Gehring
Oct 7, 2004·Genome Research·Zuzana SwigonováJoachim Messing
Oct 7, 2004·Genome Research·Jinsheng LaiJoachim Messing
Oct 8, 2004·Molecular Cell·Franck VazquezPatrice Crété
Oct 19, 2004·Genetics·Zuzana SwigonováJoachim Messing
Jan 6, 2005·Genome Research·Alex AdaiVenkatesan Sundaresan
Apr 6, 2005·Developmental Cell·Rebecca SchwabDetlef Weigel
May 11, 2005·Developmental Biology·Catherine A Kidner, Robert A Martienssen
May 28, 2005·Science·Stephen I WrightBrandon S Gaut
Jun 17, 2005·Proceedings of the National Academy of Sciences of the United States of America·Nick LauterStephen P Moose
Jul 26, 2005·Plant Physiology·Zhixin XieJames C Carrington
Jul 27, 2005·Current Opinion in Plant Biology·Matthew R Willmann, R Scott Poethig
Aug 4, 2005·Nucleic Acids Research·Ramanjulu SunkarJian-Kang Zhu

❮ Previous
Next ❯

Citations

Jun 3, 2014·BMC Plant Biology·Fenglong SunYingyin Yao
May 18, 2012·Functional & Integrative Genomics·Melda KantarUNKNOWN International Wheat Genome Sequencing Consortium
Nov 26, 2009·PLoS Genetics·Fusheng WeiRod A Wing
Nov 26, 2009·PLoS Genetics·Virginia Walbot
Apr 22, 2010·The Plant Cell·Noah FahlgrenJames C Carrington
Sep 14, 2010·Plant Physiology·Andrea L EvelandDavid Jackson
Oct 26, 2010·BMC Genomics·Moreno ColaiacovoPrimetta Faccioli
Nov 26, 2010·BMC Plant Biology·Almir S ZancaFabio T S Nogueira
Feb 18, 2011·BMC Genomics·Vivek ThakurXin-Guang Zhu
May 28, 2011·Plant Physiology·Carlos Calderón-VázquezLuis Herrera-Estrella
Jan 10, 2012·Genome Biology and Evolution·Masafumi NozawaMasatoshi Nei
Jun 19, 2012·Genome Biology·Rui XiaZongrang Liu
Jun 22, 2012·PloS One·Hai DuYi-Xiong Tang
Jan 18, 2013·BMC Genomics·Katarzyna KruszkaZofia Szweykowska-Kulinska
Jan 26, 2013·Genome Biology and Evolution·Martín Calviño, Joachim Messing
Feb 6, 2013·BMC Plant Biology·Keat Thomas TeohElizabeth E Hood
Dec 1, 2012·Molecular Genetics and Genomics : MGG·Shaopeng ZhangYonglian Zheng
Aug 3, 2012·BMC Genomics·Mingming KangJingjuan Yu
May 9, 2012·BMC Genomics·Marie TurnerSenthil Subramanian
Dec 3, 2011·Nucleic Acids Research·Michał Wojciech SzcześniakIzabela Makalowska
Oct 15, 2010·Yi chuan = Hereditas·Zhen-Hua Xu, Chuan-Xiao Xie
Nov 29, 2011·Yi chuan = Hereditas·Mao LuoGuang-Tang Pan
Mar 23, 2011·Bioinformatics·Christoph J ThiemeGünter Theissen
Oct 15, 2011·Plant Molecular Biology·Matthew W Jones-Rhoades
Nov 7, 2012·Planta·Agustina GentileMarcelo Menossi

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE17943

Methods Mentioned

BETA
PCR
Illumina sequencing
PCRs

Software Mentioned

vmatch
Ensembl Compara
GeneTree
Ensembl Compara GeneTree
Cytoscape
PHRED
Perl script
Mfold
mkvtree
DAGchainer

Related Concepts

Trending Feeds

COVID-19

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.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

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.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation 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.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.