Draft genome and transcriptome analyses of halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors

Overexpression of Rice Expansin7 (Osexpa7) Confers Enhanced Tolerance to Salt Stress in Rice

(2020) Chuluuntsetseg Jadamba et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars

(2020) Mohan Singh Rajkumar et al.   GENOMICS

DNA methylation reprogramming during seed development and its functional relevance in seed size/weight determination in chickpea

(2020) Mohan Singh Rajkumar et al.   Communications Biology

Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects

(2019) Takeshi Fukao et al.   Frontiers in Plant Science

Advances in understanding salt tolerance in rice

(2019) Showkat Ahmad Ganie et al.   THEORETICAL AND APPLIED GENETICS

MicroRNA396-mediated alteration in plant development and salinity stress response in creeping bentgrass

(2019) Shuangrong Yuan et al.   Horticulture Research

Gene Expression analysis associated with salt stress in a reciprocally crossed rice population

(2019) Samsad Razzaque et al.   Scientific Reports

NaCl induced salt adaptive changes and enhanced accumulation of 20-hydroxyecdysone in the in vitro shoot cultures of Spinacia oleracea (L.)

(2019) Niramaya S. Muchate et al.   Scientific Reports

psRNATarget: a plant small RNA target analysis server (2017 release)

(2018) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Cellulose synthase complexes display distinct dynamic behaviors during xylem transdifferentiation

(2018) Yoichiro Watanabe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

Draft genome sequence of first monocot-halophytic species Oryza coarctata reveals stress-specific genes

(2018) Tapan Kumar Mondal et al.   Scientific Reports

miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants

(2018) Zheng Kuang et al.   BIOINFORMATICS

A walk on the wild side: Oryza species as source for rice abiotic stress tolerance

(2017) Paloma Koprovski Menguer et al.   GENETICS AND MOLECULAR BIOLOGY

PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea

(2017) Urminder Singh et al.   NUCLEIC ACIDS RESEARCH

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation

(2017) Reena Narsai et al.   PLANT JOURNAL

Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size/weight determination in chickpea

(2017) Rohini Garg et al.   PLANT JOURNAL

The Amino Acid Metabolic and Carbohydrate Metabolic Pathway Play Important Roles during Salt-Stress Response in Tomato

(2017) Zhi Zhang et al.   Frontiers in Plant Science

Plant responses to flooding stress

(2016) Elena Loreti et al.   CURRENT OPINION IN PLANT BIOLOGY

Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes

(2016) Sachin Ashruba Gharat et al.   PLoS One

Overexpression of calmodulin-like (ShCML44) stress-responsive gene from Solanum habrochaites enhances tolerance to multiple abiotic stresses

(2016) Shoaib Munir et al.   Scientific Reports

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The key regulator of submergence tolerance, SUB1A , promotes photosynthetic and metabolic recovery from submergence damage in rice leaves

(2015) Jasper Benedict Alpuerto et al.   PLANT CELL AND ENVIRONMENT

Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice

(2015) Tapan Kumar Mondal et al.   PLoS One

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

(2015) Rohini Garg et al.   Scientific Reports

InterProScan 5: genome-scale protein function classification

(2014) P. Jones 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

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Over-expression of OsHsfA7 enhanced salt and drought tolerance in transgenic rice

(2013) Ai-Ling Liu et al.   BMB Reports

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Deep Transcriptome Sequencing of Wild Halophyte Rice, Porteresia coarctata, Provides Novel Insights into the Salinity and Submergence Tolerance Factors

(2013) R. Garg et al.   DNA RESEARCH

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Identification and characterization of salt-responsive microRNAs in Populus tomentosa by high-throughput sequencing

(2012) Yuanyuan Ren et al.   BIOCHIMIE

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

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

NAC transcription factors in plant abiotic stress responses

(2011) Kazuo Nakashima et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2011) Felix Krueger et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development

(2011) R. Garg et al.   PLANT PHYSIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Root Growth Inhibition and Lignification Induced by Salt Stress in Soybean

(2010) G. Y. S. Neves et al.   JOURNAL OF AGRONOMY AND CROP SCIENCE

HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana

(2010) Francesco Licausi et al.   PLANT JOURNAL

The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2/ERF Transcription Factors

(2010) K.-H. Jung et al.   PLANT PHYSIOLOGY

Arabidopsis RAP2.2: An Ethylene Response Transcription Factor That Is Important for Hypoxia Survival

(2010) M. Hinz et al.   PLANT PHYSIOLOGY

The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water

(2009) Yoko Hattori et al.   NATURE

Porteresia coarctata(Roxb.) Tateoka, a wild rice: a potential model for studying salt-stress biology in rice

(2009) SONALI SENGUPTA et al.   PLANT CELL AND ENVIRONMENT

Comparative sequence analysis ofMONOCULM1-orthologous regions in 14Oryzagenomes

(2009) Fei Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Salinity tolerance in halophytes*

(2008) Timothy J. Flowers et al.   NEW PHYTOLOGIST

Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array

(2008) A. Matsui et al.   PLANT AND CELL PHYSIOLOGY