Noncoding and coding transcriptome analysis reveals the regulation roles of long noncoding RNAs in fruit development of hot pepper (Capsicum annuum L.)

Identification and characterization of novel microRNAs for fruit development and quality in hot pepper (Capsicum annuum L.)

(2017) Zhoubin Liu et al.   GENE

Small RNA and degradome profiling reveals miRNA regulation in the seed germination of ancient eudicot Nelumbo nucifera

(2016) Jihong Hu et al.   BMC GENOMICS

Vitamin C and reducing sugars in the world collection of Capsicum baccatum L. genotypes

(2016) Venu Perla et al.   FOOD CHEMISTRY

Chlorophyll metabolism in pollinated vs. parthenocarpic fig fruits throughout development and ripening

(2016) Yogev Rosianskey et al.   PLANTA

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

Long non-coding RNAs and their functions in plants

(2015) Julia A Chekanova   CURRENT OPINION IN PLANT BIOLOGY

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

Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypiumspp.)

(2015) Maojun Wang et al.   NEW PHYTOLOGIST

Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations

(2015) Maria Helena Cruz de Carvalho et al.   NEW PHYTOLOGIST

Comprehensive analysis and expression profile of the homeodomain leucine zipper IV transcription factor family in tomato

(2015) Yanna Gao et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Transcriptional profiling of apple fruit in response to heat treatment: Involvement of a defense response during Penicillium expansum infection

(2015) A. Spadoni et al.   POSTHARVEST BIOLOGY AND TECHNOLOGY

Comparison of the expression of chlorophyll-degradation-related genes during ripening between stay-green and yellow-pear cultivars

(2015) Nongluk Charoenchongsuk et al.   SCIENTIA HORTICULTURAE

Battles and hijacks: noncoding transcription in plants

(2015) Federico Ariel et al.   TRENDS IN PLANT SCIENCE

Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

(2014) Peng Shuai et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2014) Chao Di et al.   PLANT JOURNAL

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

(2014) C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor

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

Circular RNAs: diversity of form and function

(2014) Erika Lasda et al.   RNA

Characterization of the stage dependency of high temperature on green ripening reveals a distinct chlorophyll degradation regulation in banana fruit

(2014) Lina Du et al.   SCIENTIA HORTICULTURAE

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

Flowering time control in ornamental gloxinia (Sinningia speciosa) by manipulation of miR159 expression

(2013) Xiaoyan Li et al.   ANNALS OF BOTANY

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Long non-coding genes implicated in response to stripe rust pathogen stress in wheat (Triticum aestivum L.)

(2013) Hong Zhang et al.   MOLECULAR BIOLOGY REPORTS

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

A New Tomato NAC (NAM/ATAF1/2/CUC2) Transcription Factor, SlNAC4, Functions as a Positive Regulator of Fruit Ripening and Carotenoid Accumulation

(2013) Mingku Zhu et al.   PLANT AND CELL PHYSIOLOGY

Biogenesis, Turnover, and Mode of Action of Plant MicroRNAs

(2013) K. Rogers et al.   PLANT CELL

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

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

De Novo Transcriptome Assembly in Chili Pepper (Capsicum frutescens) to Identify Genes Involved in the Biosynthesis of Capsaicinoids

(2013) Shaoqun Liu et al.   PLoS One

The Hot Pepper (Capsicum annuum) MicroRNA Transcriptome Reveals Novel and Conserved Targets: A Foundation for Understanding MicroRNA Functional Roles in Hot Pepper

(2013) Dong-Gyu Hwang et al.   PLoS One

R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

(2013) Q. Sun et al.   SCIENCE

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Small RNAs in development – insights from plants

(2012) Xuemei Chen   CURRENT OPINION IN GENETICS & DEVELOPMENT

Molecular characterization of banana NAC transcription factors and their interactions with ethylene signalling component EIL during fruit ripening

(2012) Wei Shan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2012) Cole Trapnell et al.   Nature Protocols

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

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

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

De Novo Assembly, Characterization and Functional Annotation of Pineapple Fruit Transcriptome through Massively Parallel Sequencing

(2012) Wen Dee Ong et al.   PLoS One

Multiple evidence for the role of an Ovate-like gene in determining fruit shape in pepper

(2011) Aphrodite Tsaballa et al.   BMC PLANT BIOLOGY

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

(2011) Eun-Deok Kim et al.   TRENDS IN PLANT SCIENCE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

AnOrange RipeningMutant Links Plastid NAD(P)H Dehydrogenase Complex Activity to Central and Specialized Metabolism during Tomato Fruit Maturation

(2010) Shai Nashilevitz et al.   PLANT CELL

Molecular biology of capsaicinoid biosynthesis in chili pepper (Capsicum spp.)

(2010) Cesar Aza-González et al.   PLANT CELL REPORTS

A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening

(2010) Mi-Young Chung et al.   PLANT JOURNAL

Genome-wide computational identification and manual annotation of human long noncoding RNA genes

(2010) H. Jia et al.   RNA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

(2009) Szymon Swiezewski et al.   NATURE

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

Interplay of miR164,CUP-SHAPED COTYLEDONgenes andLATERAL SUPPRESSORcontrols axillary meristem formation inArabidopsis thaliana

(2008) Smita Raman et al.   PLANT JOURNAL

MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis

(2008) Bikram Datt Pant et al.   PLANT JOURNAL

Degradation of microRNAs by a Family of Exoribonucleases in Arabidopsis

(2008) Vanitharani Ramachandran et al.   SCIENCE