PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response

Characterization and pathogenicity of six Cytospora strains causing stem canker of wild apple in the Tianshan Forest, China

(2020) Xiaojie Liu et al.   FOREST PATHOLOGY

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

(2019) Liangzhen Zhao et al.   Frontiers in Genetics

Alternative Splicing in the Regulation of Plant–Microbe Interactions

(2019) Richard Rigo et al.   PLANT AND CELL PHYSIOLOGY

MdUGT88F1-Mediated Phloridzin Biosynthesis Regulates Apple Development and Valsa Canker Resistance

(2019) Kun Zhou et al.   PLANT PHYSIOLOGY

Stressed Out About Hormones: How Plants Orchestrate Immunity

(2019) Marco Bürger et al.   Cell Host & Microbe

Plant cell surface immune receptor complex signaling

(2019) Wei-Lin Wan et al.   CURRENT OPINION IN PLANT BIOLOGY

Dextran as an elicitor of phenylpropanoid and flavonoid biosynthesis in tomato fruit against gray mold infection

(2019) Laifeng Lu et al.   CARBOHYDRATE POLYMERS

Insight into Genes Regulating Postharvest Aflatoxin Contamination of Tetraploid Peanut from Transcriptional Profiling

(2018) Walid Korani et al.   GENETICS

The developmental dynamics of the Populus stem transcriptome

(2018) Qing Chao et al.   PLANT BIOTECHNOLOGY JOURNAL

Insight into Genes Regulating Postharvest Aflatoxin Contamination of Tetraploid Peanut from Transcriptional Profiling

(2018) Walid Korani et al.   GENETICS

Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

(2018) Yuehui Chao et al.   BMC PLANT BIOLOGY

PacBio full-length cDNA sequencing integrated with RNA-seq reads drastically improves the discovery of splicing transcripts in rice

(2018) Guoqiang Zhang et al.   PLANT JOURNAL

Validation of reference genes for qRT-PCR analysis in peel and flesh of six apple cultivars (Malus domestica) at diverse stages of fruit development

(2018) Lifang Zhu et al.   SCIENTIA HORTICULTURAE

Long noncoding RNAs involve in resistance to Verticillium dahliae , a fungal disease in cotton

(2017) Lin Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

(2017) Richard Hickman et al.   PLANT CELL

Botrytis cinerea B05.10 promotes disease development in Arabidopsis by suppressing WRKY33-mediated host immunity

(2017) Shouan Liu et al.   PLANT CELL AND ENVIRONMENT

Global identification of alternative splicing via comparative analysis of SMRT- and Illumina-based RNA-seq in strawberry

(2017) Yongping Li et al.   PLANT JOURNAL

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

(2017) Naibin Duan et al.   Nature Communications

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

(2017) Jonas Korlach et al.   GigaScience

Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum

(2016) Hong Zhang et al.   BMC GENOMICS

Plant hormone-mediated regulation of stress responses

(2016) Vivek Verma et al.   BMC PLANT BIOLOGY

The Arabidopsis CERK1‐associated kinase PBL27 connects chitin perception to MAPK activation

(2016) Kenta Yamada et al.   EMBO JOURNAL

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

Apple resistance responses against Valsa mali revealed by transcriptomics analyses

(2016) Zhiyuan Yin et al.   PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY

Salicylic acid receptors activate jasmonic acid signalling through a non-canonical pathway to promote effector-triggered immunity

(2016) Lijing Liu et al.   Nature Communications

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

Metabolic response induced by parasitic plant-fungus interactions hinder amino sugar and nucleotide sugar metabolism in the host

(2016) Dong-Kyu Lee et al.   Scientific Reports

Transcription factors WRKY70 and WRKY11 served as regulators in rhizobacteriumBacillus cereusAR156-induced systemic resistance toPseudomonas syringaepv.tomatoDC3000 in Arabidopsis

(2015) Chun-Hao Jiang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome sequence ofValsacanker pathogens uncovers a potential adaptation of colonization of woody bark

(2015) Zhiyuan Yin et al.   NEW PHYTOLOGIST

Transcriptional networks in plant immunity

(2015) Kenichi Tsuda et al.   NEW PHYTOLOGIST

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Leveraging transcript quantification for fast computation of alternative splicing profiles

(2015) Gael P. Alamancos et al.   RNA

Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100

(2015) Shouan Liu et al.   eLife

Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants

(2015) Chibuikem I. N. Unamba et al.   Frontiers in Plant Science

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

RETRACTED: TheArabidopsisMalectin-Like Leucine-Rich Repeat Receptor-Like Kinase IOS1 Associates with the Pattern Recognition Receptors FLS2 and EFR and Is Critical for Priming of Pattern-Triggered Immunity

(2014) Ching-Wei Chen et al.   PLANT CELL

Transcriptome dynamics of a desert poplar (Populus pruinosa) in response to continuous salinity stress

(2014) Jian Zhang et al.   PLANT CELL REPORTS

Selective regulation of the chitin-induced defense response by the Arabidopsis receptor-like cytoplasmic kinase PBL27

(2014) Tomonori Shinya et al.   PLANT JOURNAL

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

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

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

The domestication and evolutionary ecology of apples

(2013) Amandine Cornille et al.   TRENDS IN GENETICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Highly sensitive and quantitative profiling of acidic phytohormones using derivatization approach coupled with nano-LC–ESI-Q-TOF-MS analysis

(2012) Ming-Luan Chen et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Faster sequencers, larger datasets, new challenges

(2012) Christopher E Mason et al.   GENOME BIOLOGY

Hormone Crosstalk in Plant Disease and Defense: More Than Just JASMONATE-SALICYLATE Antagonism

(2011) Alexandre Robert-Seilaniantz et al.   Annual Review of Phytopathology

Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry

(2011) Li Xu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Re-evaluation of pathogens causing Valsa canker on apple in China

(2011) Xuli Wang et al.   MYCOLOGIA

Quantitative analysis of major plant hormones in crude plant extracts by high-performance liquid chromatography–mass spectrometry

(2010) Xiangqing Pan et al.   Nature Protocols

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

WRKY transcription factors

(2010) Paul J. Rushton et al.   TRENDS IN PLANT SCIENCE

Networking by small-molecule hormones in plant immunity

(2009) Corné M J Pieterse et al.   Nature Chemical Biology

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

(2009) BJÖRN USADEL et al.   PLANT CELL AND ENVIRONMENT

The Role of WRKY Transcription Factors in Plant Immunity

(2009) S. P. Pandey et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Role of plant hormones in plant defence responses

(2008) Rajendra Bari et al.   PLANT MOLECULAR BIOLOGY

Kinetics of Salicylate-Mediated Suppression of Jasmonate Signaling Reveal a Role for Redox Modulation

(2008) A. Koornneef et al.   PLANT PHYSIOLOGY

The AP2/ERF Domain Transcription Factor ORA59 Integrates Jasmonic Acid and Ethylene Signals in Plant Defense

(2008) M. Pre et al.   PLANT PHYSIOLOGY

Structure and function of enzymes involved in the biosynthesis of phenylpropanoids

(2008) J.-L. Ferrer et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY