Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes

High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.)

(2020) Zhengmei Yang et al.   BMC GENOMICS

Aliphatic suberin confers salt tolerance to Arabidopsis by limiting Na+ influx, K+ efflux and water backflow

(2020) Pei Wang et al.   PLANT AND SOIL

Genome-wide identification of long non-coding RNAs and circular RNAs reveal their ceRNA networks in response to cucumber green mottle mosaic virus infection in watermelon

(2020) Yuyan Sun et al.   ARCHIVES OF VIROLOGY

Overexpression of PpSnRK1α in tomato enhanced salt tolerance by regulating ABA signaling pathway and reactive oxygen metabolism

(2020) Wen-Ru Wang et al.   BMC PLANT BIOLOGY

Identification of miR390-TAS3-ARF pathway in response to salt stress in Helianthus tuberosus L.

(2020) Fen Liang Wen et al.   GENE

The brassinosteroid‐responsive xyloglucan endotransglucosylase/hydrolase 19 ( XTH19 ) and XTH23 genes are involved in lateral root development under salt stress in Arabidopsis

(2020) Peipei Xu et al.   PLANT JOURNAL

Overexpression of HcSCL13, a Halostachys caspica GRAS transcription factor, enhances plant growth and salt stress tolerance in transgenic Arabidopsis

(2020) Sheng Zhang et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

How Plant Hormones Mediate Salt Stress Responses

(2020) Zipeng Yu et al.   TRENDS IN PLANT SCIENCE

Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms

(2020) He Zhao et al.   Journal of Integrative Plant Biology

MicroRNA414c affects salt tolerance of cotton by regulating reactive oxygen species metabolism under salinity stress

(2019) Wei Wang et al.   RNA Biology

A large‐scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis

(2019) Pei Zhang et al.   PLANT JOURNAL

Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene

(2019) Anning Zhang et al.   MOLECULAR BREEDING

Circular RNA hsa_circ_0001649 inhibits hepatocellular carcinoma progression via multiple miRNAs sponge

(2019) Yang Su et al.   Aging-US

Identification of cucumber circular RNAs responsive to salt stress

(2019) Yong-Xing Zhu et al.   BMC PLANT BIOLOGY

AtHSFA7b positively mediates salt stress tolerance by binding to an E-box like motif to regulate gene expression

(2019) Dandan Zang et al.   JOURNAL OF EXPERIMENTAL BOTANY

MiR319‐mediated ethylene biosynthesis, signaling and salt stress response in switchgrass

(2019) Yanrong Liu et al.   PLANT BIOTECHNOLOGY JOURNAL

Expression of the maize MYB transcription factor ZmMYB3R enhances drought and salt stress tolerance in transgenic plants

(2019) Jiandong Wu et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Overexpression of a Metallothionein 2A Gene from Date Palm Confers Abiotic Stress Tolerance to Yeast and Arabidopsis thaliana

(2019) Himanshu V. Patankar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Arabidopsis CPK6 positively regulates ABA signaling and drought tolerance through phosphorylating ABA-responsive element binding factors

(2019) Hanfeng Zhang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Chromatin remodeling for the transcription of type 2C protein phosphatase genes in response to salt stress

(2019) Nguyen Hoai Nguyen et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Transcriptome – Scale characterization of salt responsive bean TCP transcription factors

(2018) Emre İlhan et al.   GENE

MicroRNA1917 targets CTR4 splice variants to regulate ethylene responses in tomato

(2018) Yanling Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Knockdown of Rice MicroRNA166 Confers Drought Resistance by Causing Leaf Rolling and Altering Stem Xylem Development

(2018) Jinshan Zhang et al.   PLANT PHYSIOLOGY

TheMicroRNA390/TRANS-ACTING SHORT INTERFERING RNA3Module Mediates Lateral Root Growth under Salt Stress via the Auxin Pathway

(2018) Fu He et al.   PLANT PHYSIOLOGY

Short-term salt stress in Brassica rapa seedlings causes alterations in auxin metabolism

(2018) Iva Pavlović et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Identification and characterization of microRNAs in tree peony during chilling induced dormancy release by high-throughput sequencing

(2018) Yuxi Zhang et al.   Scientific Reports

Wheat miRNA TaemiR408 Acts as an Essential Mediator in Plant Tolerance to Pi Deprivation and Salt Stress via Modulating Stress-Associated Physiological Processes

(2018) Qianqian Bai et al.   Frontiers in Plant Science

Constitutive Expression of miR408 Improves Biomass and Seed Yield in Arabidopsis

(2018) Zhaoqing Song et al.   Frontiers in Plant Science

miR394 Acts as a Negative Regulator of Arabidopsis Resistance to B. cinerea Infection by Targeting LCR

(2018) Xing Tian et al.   Frontiers in Plant Science

Salinity and crop yield

(2018) C. Zörb et al.   PLANT BIOLOGY

Identification and characterization of circRNAs in Pyrus betulifolia Bunge under drought stress

(2018) Jinxing Wang et al.   PLoS One

MicroRNA319 family members play an important role in Solanum habrochaites and S. lycopersicum responses to chilling and heat stresses

(2018) X.P. Shi et al.   BIOLOGIA PLANTARUM

Characteristics of plant circular RNAs

(2018) Qinjie Chu et al.   BRIEFINGS IN BIOINFORMATICS

Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

(2018) Chunyu Cao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genome-wide identification and functional analysis of circRNAs in Zea mays

(2018) Baihua Tang et al.   PLoS One

Transcriptomic analysis reveals the importance of JA-Ile turnover in the response of Arabidopsis plants to plant growth promoting rhizobacteria and salinity

(2017) Gorka Erice et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Characterization of conserved circular RNA in polyploid Gossypium species and their ancestors

(2017) Ting Zhao et al.   FEBS LETTERS

NRT1.5/NPF7.3 Functions as a Proton-Coupled H + /K + Antiporter for K + Loading into the Xylem in Arabidopsis

(2017) Hong Li et al.   PLANT CELL

Identification of salt-stress responsive microRNAs from Solanum lycopersicum and Solanum pimpinellifolium

(2017) Gangjun Zhao et al.   PLANT GROWTH REGULATION

Laccase GhLac1 Modulates Broad-Spectrum Biotic Stress Tolerance via Manipulating Phenylpropanoid Pathway and Jasmonic Acid Synthesis

(2017) Qin Hu et al.   PLANT PHYSIOLOGY

The maize WRKY transcription factor ZmWRKY17 negatively regulates salt stress tolerance in transgenic Arabidopsis plants

(2017) Ronghao Cai et al.   PLANTA

A Wheat R2R3-type MYB Transcription Factor TaODORANT1 Positively Regulates Drought and Salt Stress Responses in Transgenic Tobacco Plants

(2017) Qiuhui Wei et al.   Frontiers in Plant Science

Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress

(2017) Yuexia Wang et al.   Frontiers in Plant Science

Genome Wide Identification and Characterization of Apple bHLH Transcription Factors and Expression Analysis in Response to Drought and Salt Stress

(2017) Ke Mao et al.   Frontiers in Plant Science

EIN3 and SOS2 synergistically modulate plant salt tolerance

(2017) Ruidang Quan et al.   Scientific Reports

Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean

(2017) Wei Zhao et al.   Scientific Reports

Deciphering the roles of circRNAs on chilling injury in tomato

(2016) Jinhua Zuo et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Circular RNAs are miRNA sponges and can be used as a new class of biomarker

(2016) Franceli Rodrigues Kulcheski et al.   JOURNAL OF BIOTECHNOLOGY

Solanum lycopersicum agamous-like MADS-box protein AGL15-like gene, SlMBP11, confers salt stress tolerance

(2016) Xuhu Guo et al.   MOLECULAR BREEDING

Plant Circular RNAs (circRNAs): Transcriptional Regulation Beyond miRNAs in Plants

(2016) Gaurav Sablok et al.   Molecular Plant

Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes

(2016) Bilgin Candar-Cakir et al.   PLANT BIOTECHNOLOGY JOURNAL

Functional Characterization of CYP94-Genes and Identification of a Novel Jasmonate Catabolite in Flowers

(2016) Viktoria Bruckhoff et al.   PLoS One

Identification of MicroRNAs and Their Targets Associated with Fruit-Bagging and Subsequent Sunlight Re-exposure in the “Granny Smith” Apple Exocarp Using High-Throughput Sequencing

(2016) Dong Qu et al.   Frontiers in Plant Science

Genome-wide identification of soybean WRKY transcription factors in response to salt stress

(2016) Yanchong Yu et al.   SpringerPlus

Differential transcript abundance of salt overly sensitive (SOS) pathway genes is a determinant of salinity stress tolerance of wheat

(2015) Lekshmy Sathee et al.   ACTA PHYSIOLOGIAE PLANTARUM

Hexaploid wheat (Triticum aestivum) root miRNome analysis in response to salt stress

(2015) H. Eren et al.   ANNALS OF APPLIED BIOLOGY

Identification of novel and salt-responsive miRNAs to explore miRNA-mediated regulatory network of salt stress response in radish (Raphanus sativus L.)

(2015) Xiaochuan Sun et al.   BMC GENOMICS

Widespread noncoding circular RNAs in plants

(2015) Chu-Yu Ye et al.   NEW PHYTOLOGIST

Elevated Levels of CYP94 Family Gene Expression Alleviate the Jasmonate Response and Enhance Salt Tolerance in Rice

(2015) Ken-ichi Kurotani et al.   PLANT AND CELL PHYSIOLOGY

Sp-miR396a-5p acts as a stress-responsive genes regulator by conferring tolerance to abiotic stresses and susceptibility to Phytophthora nicotianae infection in transgenic tobacco

(2015) Lei Chen et al.   PLANT CELL REPORTS

Wheat NAC transcription factor TaNAC29 is involved in response to salt stress

(2015) Zhongyang Xu et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa

(2015) Ira Vashisht et al.   PLANTA

Transcriptome-wide investigation of circular RNAs in rice

(2015) Tingting Lu et al.   RNA

Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

(2015) Maria Barciszewska-Pacak et al.   Frontiers in Plant Science

Salt stress differently affects growth, water status and antioxidant enzyme activities in Solanum lycopersicum and its wild relative Solanum chilense

(2014) Juan Pablo Mart�nez et al.   AUSTRALIAN JOURNAL OF BOTANY

Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

(2014) Vikas Belamkar et al.   BMC GENOMICS

Conserved miRNAs and Their Response to Salt Stress in Wild Eggplant Solanum linnaeanum Roots

(2014) Yong Zhuang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean

(2014) Senlei Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley

(2014) Katarzyna Kruszka et al.   JOURNAL OF EXPERIMENTAL BOTANY

miRNAs in the crosstalk between phytohormone signalling pathways

(2014) J. Curaba et al.   JOURNAL OF EXPERIMENTAL BOTANY

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR CELL

Transcriptomic profiling revealed an important role of cell wall remodeling and ethylene signaling pathway during salt acclimation in Arabidopsis

(2014) Xiaoyan Shen et al.   PLANT MOLECULAR BIOLOGY

Physiological responses of transgenic tobacco plants expressing the dehydration-responsive RD22 gene of Vitis vinifera to salt stress

(2014) Rahma JARDAK JAMOUSSI et al.   TURKISH JOURNAL OF BOTANY

Prediction and Expression Analysis of miRNAs Associated with Heat Stress in Oryza sativa

(2014) B. SAILAJA et al.   Rice Science

miR394 and LCR are involved in Arabidopsis salt and drought stress responses in an abscisic acid-dependent manner

(2013) Jian Song et al.   BMC PLANT BIOLOGY

Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

(2013) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

Loss of the R2R3 MYB, AtMyb73, causes hyper-induction of the SOS1 and SOS3 genes in response to high salinity in Arabidopsis

(2013) Jun Hyeok Kim et al.   JOURNAL OF PLANT PHYSIOLOGY

The Salt Overly Sensitive (SOS) Pathway: Established and Emerging Roles

(2013) Hongtao Ji et al.   Molecular Plant

Overexpression ofGmCaM4in soybean enhances resistance to pathogens and tolerance to salt stress

(2013) Suryadevara S. Rao et al.   MOLECULAR PLANT PATHOLOGY

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Endodermal ABA Signaling Promotes Lateral Root Quiescence during Salt Stress inArabidopsisSeedlings

(2013) Lina Duan et al.   PLANT CELL

Global identification of miRNAs and targets in Populus euphratica under salt stress

(2013) Bosheng Li et al.   PLANT MOLECULAR BIOLOGY

Constitutive Expression of a miR319 Gene Alters Plant Development and Enhances Salt and Drought Tolerance in Transgenic Creeping Bentgrass

(2013) M. Zhou et al.   PLANT PHYSIOLOGY

A novel tomato MYC-type ICE1-like transcription factor, SlICE1a, confers cold, osmotic and salt tolerance in transgenic tobacco

(2013) Hai-Long Feng et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

microRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.)

(2012) Anca Macovei et al.   BMC PLANT BIOLOGY

Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa

(2012) Lei Chen et al.   GENE

Expression profile of miRNAs in Populus cathayana L. and Salix matsudana Koidz under salt stress

(2012) Jing Zhou et al.   MOLECULAR BIOLOGY REPORTS

Salt Stress Triggers Phosphorylation of the Arabidopsis Vacuolar K+ Channel TPK1 by Calcium-Dependent Protein Kinases (CDPKs)

(2012) Andreas Latz et al.   Molecular Plant

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Dual-Level Regulation of ACC Synthase Activity by MPK3/MPK6 Cascade and Its Downstream WRKY Transcription Factor during Ethylene Induction in Arabidopsis

(2012) Guojing Li et al.   PLoS Genetics

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

(2011) Tianzuo Wang et al.   BMC GENOMICS

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa

(2011) Xiang Yu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity

(2011) Zujun Yin et al.   MOLECULAR BIOLOGY REPORTS

Salt and Drought Stresses Induce the Aberrant Expression of microRNA Genes in Tobacco

(2011) Taylor P. Frazier et al.   MOLECULAR BIOTECHNOLOGY

Arabidopsis 3-Ketoacyl-CoA Thiolase-2 (KAT2), an Enzyme of Fatty Acid β-Oxidation, is Involved in ABA Signal Transduction

(2011) Tao Jiang et al.   PLANT AND CELL PHYSIOLOGY

Expression and tissue-specific localization of nitrate-responsive miRNAs in roots of maize seedlings

(2011) SARA TREVISAN et al.   PLANT CELL AND ENVIRONMENT

Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants

(2011) Yu-Jun Hao et al.   PLANT JOURNAL

Activation of the plasma membrane Na/H antiporter Salt-Overly-Sensitive 1 (SOS1) by phosphorylation of an auto-inhibitory C-terminal domain

(2011) F. J. Quintero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cytochrome P450 CYP94B3 mediates catabolism and inactivation of the plant hormone jasmonoyl-L-isoleucine

(2011) A. J. K. Koo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Laccase-catalysed oxidations of naturally occurring phenols: from in vivo biosynthetic pathways to green synthetic applications

(2011) Jong-Rok Jeon et al.   Microbial Biotechnology

ABA and GA signaling pathways interact and regulate seed germination and seedling development under salt stress

(2010) Kun Yuan et al.   ACTA PHYSIOLOGIAE PLANTARUM

Four abiotic stress-induced miRNA families differentially regulated in the embryogenic and non-embryogenic callus tissues of Larix leptolepis

(2010) Shougong Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The Physiological, Biochemical and Molecular Roles of Brassinosteroids and Salicylic Acid in Plant Processes and Salt Tolerance

(2010) M. Ashraf et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Gibberellic acid mediated induction of salt tolerance in wheat plants: Growth, ionic partitioning, photosynthesis, yield and hormonal homeostasis

(2010) Muhammad Iqbal et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

The salt- and drought-inducible poplar GRAS protein SCL7 confers salt and drought tolerance in Arabidopsis thaliana

(2010) Hong-Shuang Ma et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa

(2010) Liguo Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

miR171 Family Members are Involved in Drought Response in Solanum tuberosum

(2010) Eul-Won Hwang et al.   JOURNAL OF PLANT BIOLOGY

Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses

(2010) Jianqiang Shen et al.   MOLECULAR GENETICS AND GENOMICS

Effect of Nitrate on Root Development and Nitrogen Uptake of Suaeda physophora Under NaCl Salinity

(2010) Jun-Feng YUAN et al.   PEDOSPHERE

The Mg-Chelatase H Subunit ofArabidopsisAntagonizes a Group of WRKY Transcription Repressors to Relieve ABA-Responsive Genes of Inhibition

(2010) Yi Shang et al.   PLANT CELL

H2O2 and cytosolic Ca2+ signals triggered by the PM H+-coupled transport system mediate K+/Na+ homeostasis in NaCl-stressed Populus euphratica cells

(2010) JIAN SUN et al.   PLANT CELL AND ENVIRONMENT

Hydrogen peroxide and nitric oxide mediate K+/Na+ homeostasis and antioxidant defense in NaCl-stressed callus cells of two contrasting poplars

(2010) Jian Sun et al.   PLANT CELL TISSUE AND ORGAN CULTURE

miRNA expression patterns of Triticum dicoccoides in response to shock drought stress

(2010) Melda Kantar et al.   PLANTA

Effect of NaCl on leaf H+-ATPase and the relevance to salt tolerance in two contrasting poplar species

(2010) Xiuying Ma et al.   TREES-STRUCTURE AND FUNCTION

Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor

(2009) Botao Zhao et al.   BMC MOLECULAR BIOLOGY

Identification of novel stress-regulated microRNAs from Oryza sativa L.

(2009) Xinyu Jian et al.   GENOMICS

Effects of NO 3 − -N on the growth and salinity tolerance of Tamarix laxa Willd

(2009) Xiaodong Ding et al.   PLANT AND SOIL

A Novel Plant Leucine-Rich Repeat Receptor Kinase Regulates the Response of Medicago truncatula Roots to Salt Stress

(2009) L. de Lorenzo et al.   PLANT CELL

AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation

(2009) Takuya Yoshida et al.   PLANT JOURNAL

CYP86B1 Is Required for Very Long Chain  -Hydroxyacid and  , -Dicarboxylic Acid Synthesis in Root and Seed Suberin Polyester

(2009) V. Compagnon et al.   PLANT PHYSIOLOGY

Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis

(2009) Guru Jagadeeswaran et al.   PLANTA

Differential expression of miRNAs in response to salt stress in maize roots

(2008) Dong Ding et al.   ANNALS OF BOTANY

MicroRNA-mediated Systemic Down-regulation of Copper Protein Expression in Response to Low Copper Availability inArabidopsis

(2008) Salah E. Abdel-Ghany et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Arabidopsis cytochrome P450 CYP86A1 encodes a fatty acid ω-hydroxylase involved in suberin monomer biosynthesis

(2008) Rene Höfer et al.   JOURNAL OF EXPERIMENTAL BOTANY

Overexpression of SOS (Salt Overly Sensitive) Genes Increases Salt Tolerance in Transgenic Arabidopsis

(2008) Qing Yang et al.   Molecular Plant

Arabidopsis PPR40 Connects Abiotic Stress Responses to Mitochondrial Electron Transport

(2008) L. Zsigmond et al.   PLANT PHYSIOLOGY

NaCl-Induced Alternations of Cellular and Tissue Ion Fluxes in Roots of Salt-Resistant and Salt-Sensitive Poplar Species

(2008) J. Sun et al.   PLANT PHYSIOLOGY

Isolation and identification of two genes encoding leucine-rich repeat (LRR) proteins differentially responsive to pathogen attack and salt stress in tobacco

(2008) Zhao-Shi Xu et al.   PLANT SCIENCE

Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana

(2008) H.-H. Liu et al.   RNA