Global identification of long non-coding RNAs involved in the induction of spinach flowering

Identification and characterization of regulatory pathways involved in early flowering in the new leaves of alfalfa (Medicago sativa L.) by transcriptome analysis

(2021) Dongmei Ma et al.   BMC PLANT BIOLOGY

Transcriptome architecture reveals genetic networks of bolting regulation in spinach

(2021) Reza Abolghasemi et al.   BMC PLANT BIOLOGY

Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum

(2021) Pooja Moni Baruah et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Computational Identification of miRNAs and Temperature-Responsive lncRNAs From Mango (Mangifera indica L.)

(2021) Nann Miky Moh Moh et al.   Frontiers in Genetics

Comparative transcriptome analysis uncovers regulatory roles of long non-coding RNAs involved in resistance to powdery mildew in melon

(2020) Chao Gao et al.   BMC GENOMICS

The sugar transporter SWEET10 acts downstream of FLOWERING LOCUS T during floral transition of Arabidopsis thaliana

(2020) Fernando Andrés et al.   BMC PLANT BIOLOGY

Structure, Regulation, and Function of Linear and Circular Long Non-Coding RNAs

(2020) Tao Qin et al.   Frontiers in Genetics

The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System

(2020) Weigang Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptome Analysis of Carbohydrate Metabolism Genes and Molecular Regulation of Sucrose Transport Gene LoSUT on the Flowering Process of Developing Oriental Hybrid Lily ‘Sorbonne’ Bulb

(2020) Jiahui Gu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Functional classification of plant long noncoding RNAs: a transcript is known by the company it keeps

(2020) Leandro Lucero et al.   NEW PHYTOLOGIST

PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs

(2020) Jingjing Jin et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Identification and Characterization of APETALA2/Ethylene-Responsive Element Binding Factor Superfamily Genes in Soybean Seed Development

(2020) Wenbo Jiang et al.   Frontiers in Plant Science

Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L

(2020) Ning Li et al.   BMC GENOMICS

LncRNA expression profile and ceRNA analysis in tomato during flowering

(2019) Zhenchao Yang et al.   PLoS One

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis

(2019) Verónica Jiménez-Jacinto et al.   Frontiers in Genetics

Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume

(2019) Xinxin Wu et al.   BMC PLANT BIOLOGY

Bolting, an Important Process in Plant Development, Two Types in Plants

(2019) Chen Chen et al.   JOURNAL OF PLANT BIOLOGY

Identification and genetic analysis of alternative splicing of long non-coding RNAs in tomato initial flowering stage

(2019) Zhenchao Yang et al.   GENOMICS

Tissue specific long non-coding RNAs are involved in aroma formation of black tea

(2019) Deepti Varshney et al.   INDUSTRIAL CROPS AND PRODUCTS

PRECOCIOUS 1 ( POCO 1), a mitochondrial pentatricopeptide repeat protein affects flowering time in Arabidopsis thaliana

(2019) Hossein Emami et al.   PLANT JOURNAL

Proteomic Analysis of Shoot Tips from Two Alfalfa Cultivars with Different Florescence

(2019) Hao Sun et al.   PLANT MOLECULAR BIOLOGY REPORTER

Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica

(2019) Natalia Gomes Vieira et al.   Scientific Reports

Long noncoding RNAs in Brassica rapa L. following vernalization

(2019) Daniel J. Shea et al.   Scientific Reports

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

(2019) Xiaobo Zhao et al.   Genes

Transcriptome analysis of bolting in A. tequilana reveals roles for florigen, MADS, fructans and gibberellins

(2019) Emmanuel Avila de Dios et al.   BMC GENOMICS

Knockout of Arabidopsis Serotonin N-Acetyltransferase-2 Reduces Melatonin Levels and Delays Flowering

(2019) Hyoung Yool Lee et al.   Biomolecules

Prediction of plant lncRNA by ensemble machine learning classifiers

(2018) Caitlin M. A. Simopoulos et al.   BMC GENOMICS

Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages

(2018) Wenqiang Fan et al.   BMC PLANT BIOLOGY

Arabidopsis thaliana ambient temperature responsive lncRNAs

(2018) Edouard Severing et al.   BMC PLANT BIOLOGY

Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants

(2018) Tatianne da Costa Negri et al.   BRIEFINGS IN BIOINFORMATICS

Feedback regulation of COOLAIR expression controls seed dormancy and flowering time

(2018) Min Chen et al.   SCIENCE

LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments

(2018) Peng Wang et al.   NUCLEIC ACIDS RESEARCH

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

lncRNA profile study reveals the mRNAs and lncRNAs associated with docetaxel resistance in breast cancer cells

(2018) Peide Huang et al.   Scientific Reports

The antiphasic regulatory module comprising CDF5 and its antisense RNA FLORE links the circadian clock to photoperiodic flowering

(2017) Rossana Henriques et al.   NEW PHYTOLOGIST

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

(2017) Yu-Jian Kang et al.   NUCLEIC ACIDS RESEARCH

E3 Ubiquitin Ligases: Ubiquitous Actors in Plant Development and Abiotic Stress Responses

(2017) Kai Shu et al.   PLANT AND CELL PHYSIOLOGY

The control of flowering time by environmental factors

(2017) Lae-Hyeon Cho et al.   PLANT JOURNAL

Overexpression of Arabidopsis FLOWERING LOCUS T (FT) gene improves floral development in cassava (Manihot esculenta, Crantz)

(2017) O. Sarah Adeyemo et al.   PLoS One

Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

(2017) Chenxi Xu et al.   Nature Communications

Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken

(2017) Tao Zhang et al.   PLoS One

Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.)

(2017) Chen-Yang Wang et al.   Scientific Reports

De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering

(2016) Shanshan Nie et al.   BMC GENOMICS

Arabidopsis ubiquitin-conjugating enzyme UBC22 is required for female gametophyte development and likely involved in Lys11-linked ubiquitination

(2016) Sheng Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

PceRBase: a database of plant competing endogenous RNA

(2016) Chunhui Yuan et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Characterising genes associated with flowering time in carrot (Daucus carotaL.) using transcriptome analysis

(2016) C.-G. Ou et al.   PLANT BIOLOGY

Association mapping of leaf traits in spinach (Spinacia oleraceaL.)

(2016) Jianbing Ma et al.   PLANT BREEDING

CHD3 chromatin-remodeling factor PICKLE regulates floral transition partially via modulating LEAFY expression at the chromatin level in Arabidopsis

(2016) Xing Fu et al.   Science China-Life Sciences

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

(2016) Emily J. Hawkes et al.   Cell Reports

MADS-Box Genes and Gibberellins Regulate Bolting in Lettuce (Lactuca sativa L.)

(2016) Yingyan Han et al.   Frontiers in Plant Science

Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development

(2015) Chunying Kang et al.   BMC GENOMICS

RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening

(2015) Benzhong Zhu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Regulation of flowering time in rice

(2015) Yang-Seok Lee et al.   JOURNAL OF PLANT BIOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14

(2015) Yong-Qiang Ning et al.   NUCLEIC ACIDS RESEARCH

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

Distinct regulation in inflorescence carbohydrate metabolism according to grapevine cultivars during floral development

(2015) Mélodie Sawicki et al.   PHYSIOLOGIA PLANTARUM

A Casparian strip domain-like gene, CASPL, negatively alters growth and cold tolerance

(2015) Jinghua Yang et al.   Scientific Reports

K-homology Nuclear Ribonucleoproteins Regulate Floral Organ Identity and Determinacy in Arabidopsis

(2015) Encarnación Rodríguez-Cazorla et al.   PLoS Genetics

Overexpression of the CC-type glutaredoxin, OsGRX6 affects hormone and nitrogen status in rice plants

(2015) Ashraf El-Kereamy et al.   Frontiers in Plant Science

Long Non-coding RNAs and Their Biological Roles in Plants

(2015) Xue Liu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

(2015) Jinyan Wang et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

GIGANTUS1 (GTS1), a member of Transducin/WD40 protein superfamily, controls seed germination, growth and biomass accumulation through ribosome-biogenesis protein interactions in Arabidopsis thaliana

(2014) Emma W Gachomo et al.   BMC PLANT BIOLOGY

cytoHubba: identifying hub objects and sub-networks from complex interactome

(2014) Chia-Hao Chin et al.   BMC Systems Biology

LncTar: a tool for predicting the RNA targets of long noncoding RNAs

(2014) Jianwei Li et al.   BRIEFINGS IN BIOINFORMATICS

Elements and machinery of non-coding RNAs: toward their taxonomy

(2014) T. Hirose et al.   EMBO REPORTS

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

Characterization of stress-responsive lncRNAs inArabidopsis thalianaby integrating expression, epigenetic and structural features

(2014) Chao Di et al.   PLANT JOURNAL

AntisenseCOOLAIRmediates the coordinated switching of chromatin states atFLCduring vernalization

(2014) Tibor Csorba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light

(2014) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional interactions among microRNAs and long noncoding RNAs

(2014) Je-Hyun Yoon et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Construction and validation of a gene co-expression network in grapevine (Vitis vinifera. L.)

(2014) Ying-Hai Liang et al.   Horticulture Research

Long noncoding RNAs: New regulators in plant development

(2013) Yu-Chan Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The Arabidopsis Cysteine-Rich GASA5 Is a Redox-Active Metalloprotein that Suppresses Gibberellin Responses

(2013) Lior Rubinovich et al.   Molecular Plant

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

(2013) H.-J. Wu et al.   PLANT PHYSIOLOGY

Cross-Repressive Interactions between SOC1 and the GATAs GNC and GNL/CGA1 in the Control of Greening, Cold Tolerance, and Flowering Time in Arabidopsis

(2013) R. Richter et al.   PLANT PHYSIOLOGY

PHYTOCHROME-DEPENDENT LATE-FLOWERING accelerates flowering through physical interactions with phytochrome B and CONSTANS

(2013) M. Endo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Effect of Organic and Conventional Cropping Systems on Ascorbic Acid, Vitamin C, Flavonoids, Nitrate, and Oxalate in 27 Varieties of Spinach (Spinacia oleracea L.)

(2012) Eunmi Koh et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Transcription factor PIF4 controls the thermosensory activation of flowering

(2012) S. Vinod Kumar et al.   NATURE

UGT87A2, an Arabidopsis glycosyltransferase, regulates flowering time viaFLOWERING LOCUS C

(2012) Bo Wang et al.   NEW PHYTOLOGIST

PsRobot: a web-based plant small RNA meta-analysis toolbox

(2012) Hua-Jun Wu et al.   NUCLEIC ACIDS RESEARCH

Structural and Functional Analysis of VQ Motif-Containing Proteins in Arabidopsis as Interacting Proteins of WRKY Transcription Factors

(2012) Y. Cheng et al.   PLANT PHYSIOLOGY

Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

(2012) Susan Boerner et al.   PLoS One

FLOWERING BHLH transcriptional activators control expression of the photoperiodic flowering regulator CONSTANS in Arabidopsis

(2012) S. Ito et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

(2012) J. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic resources collections of leafy vegetables (lettuce, spinach, chicory, artichoke, asparagus, lamb’s lettuce, rhubarb and rocket salad): composition and gaps

(2011) R. van Treuren et al.   GENETIC RESOURCES AND CROP EVOLUTION

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Regulation of flowering time and floral patterning by miR172

(2010) Qian-Hao Zhu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

The Sequential Action of miR156 and miR172 Regulates Developmental Timing in Arabidopsis

(2009) Gang Wu et al.   CELL

GASA5, a regulator of flowering time and stem growth in Arabidopsis thaliana

(2009) Shengchun Zhang et al.   PLANT MOLECULAR BIOLOGY

Repression of FLOWERING LOCUS T Chromatin by Functionally Redundant Histone H3 Lysine 4 Demethylases in Arabidopsis

(2009) Ju-Hee Jeong et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

COP1 and ELF3 Control Circadian Function and Photoperiodic Flowering by Regulating GI Stability

(2008) Jae-Woong Yu et al.   MOLECULAR CELL

ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases

(2008) Edward Kraft et al.   PLANT JOURNAL