Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening

(2018) Yoshihito Shinozaki et al.   Nature Communications

Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance toPhytophthora infestansby co-expressing glutaredoxin

(2017) Jun Cui et al.   PLANT JOURNAL

Profiling microRNA expression during multi-staged date palm ( Phoenix dactylifera L.) fruit development

(2015) Chengqi Xin et al.   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

Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato

(2015) Xin Wang et al.   NEW PHYTOLOGIST

Long noncoding RNA transcriptome of plants

(2015) Jun Liu et al.   PLANT BIOTECHNOLOGY JOURNAL

Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development

(2015) Mei-Qing Xing et al.   PLANT PHYSIOLOGY

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development

(2015) Richard J. Pattison et al.   PLANT PHYSIOLOGY

A DEMETER-like DNA demethylase governs tomato fruit ripening

(2015) Ruie Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Control of Chromatin Structure by Long Noncoding RNA

(2015) Gudrun Böhmdorfer et al.   TRENDS IN CELL BIOLOGY

Long Non-coding RNAs and Their Biological Roles in Plants

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

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

(2014) H. Wang et al.   GENOME RESEARCH

Role of plant hormones and their interplay in development and ripening of fleshy fruits

(2014) Rahul Kumar et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis

(2014) Yuqiu Wang et al.   Molecular Plant

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

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

(2014) Chao Di et al.   PLANT JOURNAL

The Exosome and Trans-Acting Small Interfering RNAs Regulate Cuticular Wax Biosynthesis during Arabidopsis Inflorescence Stem Development

(2014) Patricia Lam et al.   PLANT PHYSIOLOGY

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

(2014) Lin Li et al.   GENOME BIOLOGY

Rice epigenomics and epigenetics: challenges and opportunities

(2013) Xiangsong Chen et al.   CURRENT OPINION IN 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

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

Long noncoding RNAs responsive toFusarium oxysporuminfection inArabidopsis thaliana

(2013) Qian-Hao Zhu et al.   NEW PHYTOLOGIST

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

Long noncoding RNAs in development and disease of the central nervous system

(2013) Shi-Yan Ng et al.   TRENDS IN GENETICS

Plants regenerated from tissue culture contain stable epigenome changes in rice

(2013) Hume Stroud et al.   eLife

Long noncoding RNAs in C. elegans

(2012) J.-W. Nam et al.   GENOME RESEARCH

A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa

(2012) Ting-Ting Liu et al.   Molecular Plant

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) J. Liu et al.   PLANT CELL

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

(2012) Susan Boerner et al.   PLoS One

Genetics and Control of Tomato Fruit Ripening and Quality Attributes

(2011) Harry J. Klee et al.   Annual Review of Genetics

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

(2011) Mingming Xin et al.   BMC PLANT BIOLOGY

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

RIN transcription factor plays an important role in ethylene biosynthesis of tomato fruit ripening

(2011) Ling Li et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Tissue- and Cell-Type Specific Transcriptome Profiling of Expanding Tomato Fruit Provides Insights into Metabolic and Regulatory Specialization and Cuticle Formation

(2011) Antonio J. Matas et al.   PLANT CELL

The Tomato MADS-Box Transcription Factor RIPENING INHIBITOR Interacts with Promoters Involved in Numerous Ripening Processes in a COLORLESS NONRIPENING-Dependent Manner

(2011) C. Martel et al.   PLANT PHYSIOLOGY

Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor ( nor, rin ) and Ethylene Receptor ( Nr ) Mutants Reveals Novel Regulatory Interactions

(2011) Sonia Osorio et al.   PLANT PHYSIOLOGY

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Over-expression of sly-miR156a in tomato results in multiple vegetative and reproductive trait alterations and partial phenocopy of thesftmutant

(2010) Xiaohui Zhang et al.   FEBS LETTERS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

(2009) Gang Wu et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

(2008) S. Moxon et al.   GENOME RESEARCH

Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors

(2008) Eugenio Butelli et al.   NATURE BIOTECHNOLOGY

Amino Acid Substitutions in Homologs of the STAY-GREEN Protein Are Responsible for the green-flesh and chlorophyll retainer Mutations of Tomato and Pepper

(2008) C. S. Barry et al.   PLANT PHYSIOLOGY