Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea

RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.)

(2018) Keyvan Mahdavi Mashaki et al.   PLoS One

Genome-Wide Identification, Characterization, and Expression Analysis of Small RNA Biogenesis Purveyors Reveal Their Role in Regulation of Biotic Stress Responses in Three Legume Crops

(2017) Vanika Garg et al.   Frontiers in Plant Science

A Novel Soybean Dirigent Gene GmDIR22 Contributes to Promotion of Lignan Biosynthesis and Enhances Resistance to Phytophthora sojae

(2017) Ninghui Li et al.   Frontiers in Plant Science

Genetic Analysis of NBS-LRR Gene Family in Chickpea and Their Expression Profiles in Response to Ascochyta Blight Infection

(2017) Mandeep S. Sagi et al.   Frontiers in Plant Science

Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height

(2017) Aqin Cao et al.   PLoS One

Integrated analysis of tobacco miRNA and mRNA expression profiles under PVY infection provids insight into tobacco-PVY interactions

(2017) Yushuang Guo et al.   Scientific Reports

Chickpea-Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies

(2017) Medha L. Upasani et al.   Scientific Reports

Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi

(2016) Slavica Matić et al.   BMC GENOMICS

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

GhATAF1, a NAC transcription factor, confers abiotic and biotic stress responses by regulating phytohormonal signaling networks

(2016) Xin He et al.   PLANT CELL REPORTS

Defence gene expression profiling to Ascochyta rabiei aggressiveness in chickpea

(2016) Audrey E. Leo et al.   THEORETICAL AND APPLIED GENETICS

An Update on Genetic Resistance of Chickpea to Ascochyta Blight

(2016) Mamta Sharma et al.   Agronomy-Basel

Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea

(2016) Rohini Garg et al.   Scientific Reports

Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars

(2015) Mukesh Jain et al.   MOLECULAR BREEDING

High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea

(2015) Sangeeta Srivastava et al.   PLANT SCIENCE

To grow old: regulatory role of ethylene and jasmonic acid in senescence

(2015) Joonyup Kim et al.   Frontiers in Plant Science

Transcriptome Analysis of Early Responsive Genes in Rice during Magnaporthe oryzae Infection

(2015) Yiming Wang et al.   Plant Pathology Journal

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing

(2014) Mukesh Jain et al.   JOURNAL OF EXPERIMENTAL BOTANY

miR482 Regulation of NBS-LRR Defense Genes during Fungal Pathogen Infection in Cotton

(2014) Qian-Hao Zhu et al.   PLoS One

Identification and Characterization of Wilt and Salt Stress-Responsive MicroRNAs in Chickpea through High-Throughput Sequencing

(2014) Deshika Kohli et al.   PLoS One

Marker-Assisted Backcrossing to Introgress Resistance to Fusarium Wilt Race 1 and Ascochyta Blight in C 214, an Elite Cultivar of Chickpea

(2014) R. K. Varshney et al.   Plant Genome

Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.)

(2013) Murali Mohan Sabbavarapu et al.   EUPHYTICA

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Identification and Comparative Analysis of Cadmium Tolerance-Associated miRNAs and Their Targets in Two Soybean Genotypes

(2013) Xiaolong Fang et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

(2012) Limin Fu et al.   BIOINFORMATICS

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

(2012) Cole Trapnell et al.   Nature Protocols

A MicroRNA Superfamily Regulates Nucleotide Binding Site-Leucine-Rich Repeats and Other mRNAs

(2012) P. V. Shivaprasad et al.   PLANT CELL

Development of screening techniques and identification of new sources of resistance to Ascochyta blight disease of chickpea

(2011) S. Pande et al.   AUSTRALASIAN PLANT PATHOLOGY

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

(2011) Xiaozeng Yang et al.   BIOINFORMATICS

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Evidence of unique and shared responses to major biotic and abiotic stresses in chickpea

(2010) Nitin L. Mantri et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Involvement of Salicylate and Jasmonate Signaling Pathways inArabidopsisInteraction withFusarium graminearum

(2010) Ragiba Makandar et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Coherent but overlapping expression of microRNAs and their targets during vertebrate development

(2009) A. Shkumatava et al.   GENES & DEVELOPMENT

TheArabidopsisATAF1, a NAC Transcription Factor, Is a Negative Regulator of Defense Responses Against Necrotrophic Fungal and Bacterial Pathogens

(2009) Xiao'e Wang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

BatchPrimer3: A high throughput web application for PCR and sequencing primer design

(2008) Frank M You et al.   BMC BIOINFORMATICS

Identification of novel and candidate miRNAs in rice by high throughput sequencing

(2008) Ramanjulu Sunkar et al.   BMC PLANT BIOLOGY

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

Criteria for Annotation of Plant MicroRNAs

(2008) B. C. Meyers et al.   PLANT CELL