Extremophiles as a Model of a Natural Ecosystem: Transcriptional Coordination of Genes Reveals Distinct Selective Responses of Plants Under Climate Change Scenarios

Future warming increases probability of globally synchronized maize production shocks

(2018) Michelle Tigchelaar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of environmental changes on vegetable and legume yields and nutritional quality

(2018) Pauline F. D. Scheelbeek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome profiling during mangrove viviparity in response to abscisic acid

(2018) Liwei Hong et al.   Scientific Reports

Population genetic structure, introgression, and hybridization in the genus Rhizophora along the Brazilian coast

(2018) Patrícia M. Francisco et al.   Ecology and Evolution

Regulation of Na+ and K+ homeostasis in plants: towards improved salt stress tolerance in crop plants

(2017) Diego M. Almeida et al.   GENETICS AND MOLECULAR BIOLOGY

Temperature increase reduces global yields of major crops in four independent estimates

(2017) Chuang Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments

(2017) Wuxia Guo et al.   Frontiers in Plant Science

The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole genome sequencing

(2017) Shaohua Xu et al.   National Science Review

Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-Pseudomonas pathosystem

(2017) Marina A. Pombo et al.   Scientific Reports

Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis

(2017) Pannaga Krishnamurthy et al.   Scientific Reports

Climate changes in mangrove forests and salt marshes

(2016) Yara Schaeffer-Novelli et al.   BRAZILIAN JOURNAL OF OCEANOGRAPHY

Plant senescence and proteolysis: two processes with one destiny

(2016) Mercedes Diaz-Mendoza et al.   GENETICS AND MOLECULAR BIOLOGY

Transcriptomes of eight Arabidopsis thaliana accessions reveal core conserved, genotype- and organ-specific responses to flooding stress

(2016) Hans Van Veen et al.   PLANT PHYSIOLOGY

Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress

(2016) Paul J Zwack et al.   PLANT PHYSIOLOGY

Fatty Acid and Lipid Transport in Plant Cells

(2016) Nannan Li et al.   TRENDS IN PLANT SCIENCE

Quality Control of Photosystem II: The Mechanisms for Avoidance and Tolerance of Light and Heat Stresses are Closely Linked to Membrane Fluidity of the Thylakoids

(2016) Yasusi Yamamoto   Frontiers in Plant Science

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

(2016) Yu-Bin Yan et al.   Frontiers in Plant Science

The Plant Cell Wall: A Complex and Dynamic Structure As Revealed by the Responses of Genes under Stress Conditions

(2016) Kelly Houston et al.   Frontiers in Plant Science

Disaster risk indicators in Brazil: A proposal based on the world risk index

(2016) Lutiane Queiroz de Almeida et al.   International Journal of Disaster Risk Reduction

Tolerance and responsive gene expression of Sogatella furcifera under extreme temperature stresses are altered by its vectored plant virus

(2016) Donglin Xu et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones

(2015) Yuchen Yang et al.   BMC GENOMICS

Integrating physiological threshold experiments with climate modeling to project mangrove species’ range expansion

(2015) Kyle C. Cavanaugh et al.   GLOBAL CHANGE BIOLOGY

De novo assembly of the transcriptomes of two yellow mangroves, Ceriops tagal and C. zippeliana, and one of their terrestrial relatives, Pellacalyx yunnanensis

(2015) Yuchen Yang et al.   Marine Genomics

Barley: a translational model for adaptation to climate change

(2015) Ian K. Dawson et al.   NEW PHYTOLOGIST

Ethylene Response Factors: A Key Regulatory Hub in Hormone and Stress Signaling

(2015) Maren Müller et al.   PLANT PHYSIOLOGY

Chromatin changes in response to drought, salinity, heat, and cold stresses in plants

(2015) Jong-Myong Kim et al.   Frontiers in Plant Science

Multiple-Geographic-Scale Genetic Structure of Two Mangrove Tree Species: The Roles of Mating System, Hybridization, Limited Dispersal and Extrinsic Factors

(2015) Gustavo M. Mori et al.   PLoS One

Regulation of water balance in mangroves

(2014) Ruth Reef et al.   ANNALS OF BOTANY

Regulation of amino acid metabolic enzymes and transporters in plants

(2014) Réjane Pratelli et al.   JOURNAL OF EXPERIMENTAL BOTANY

ArabidopsisHSP90 protein modulates RPP4-mediated temperature-dependent cell death and defense responses

(2014) Fei Bao et al.   NEW PHYTOLOGIST

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Signalling crosstalk in light stress and immune reactions in plants

(2014) A. Trotta et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

HSP90s are required for NLR immune receptor accumulation in Arabidopsis

(2014) Shuai Huang et al.   PLANT JOURNAL

The cuticle and plant defense to pathogens

(2014) Mario Serrano et al.   Frontiers in Plant Science

Mangrove expansion and salt marsh decline at mangrove poleward limits

(2013) Neil Saintilan et al.   GLOBAL CHANGE BIOLOGY

Temperatures and the growth and development of maize and rice: a review

(2013) Berta Sánchez et al.   GLOBAL CHANGE BIOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Osmotic Stress Responses and Plant Growth Controlled by Potassium Transporters in Arabidopsis

(2013) Y. Osakabe et al.   PLANT CELL

Polyploids Exhibit Higher Potassium Uptake and Salinity Tolerance in Arabidopsis

(2013) D.-Y. Chao et al.   SCIENCE

Getting to the roots of it: Genetic and hormonal control of root architecture

(2013) Janelle K. H. Jung et al.   Frontiers in Plant Science

Genetic population structure of red mangrove (Rhizophora mangle L.) along the northwestern coast of Mexico

(2012) Eduardo Sandoval-Castro et al.   AQUATIC BOTANY

On the relationship between non-photochemical quenching and photoprotection of Photosystem II

(2012) Petar H. Lambrev et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Fission and proliferation of peroxisomes

(2012) M. Schrader et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Southern limit of the Western South Atlantic mangroves: Assessment of the potential effects of global warming from a biogeographical perspective

(2012) Mário Luiz Gomes Soares et al.   ESTUARINE COASTAL AND SHELF SCIENCE

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

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

Postglacial north-south expansion of populations of Rhizophora mangle (Rhizophoraceae) along the Brazilian coast revealed by microsatellite analysis

(2011) Maria W. Pil et al.   AMERICAN JOURNAL OF BOTANY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Long-term changes in the production by estuarine macrobenthos affected by multiple stressors

(2011) M. Dolbeth et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Structure of the Chloroplast NADH Dehydrogenase-Like Complex: Nomenclature for Nuclear-Encoded Subunits

(2011) K. Ifuku et al.   PLANT AND CELL PHYSIOLOGY

The Cytosolic/Nuclear HSC70 and HSP90 Molecular Chaperones Are Important for Stomatal Closure and Modulate Abscisic Acid-Dependent Physiological Responses in Arabidopsis

(2011) M. Clement et al.   PLANT PHYSIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Brassinosteroid-mediated stress tolerance in Arabidopsis shows interactions with abscisic acid, ethylene and salicylic acid pathways

(2010) Uday K Divi et al.   BMC PLANT BIOLOGY

Status and distribution of mangrove forests of the world using earth observation satellite data

(2010) C. Giri et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

A Subset of Cytokinin Two-component Signaling System Plays a Role in Cold Temperature Stress Response inArabidopsis

(2010) Jin Jeon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

New Insights into the Shikimate and Aromatic Amino Acids Biosynthesis Pathways in Plants

(2010) Vered Tzin et al.   Molecular Plant

The 26S Proteasome Function and Hsp90 Activity Involved in the Regulation of HsfA2 Expression in Response to Oxidative Stress

(2010) Ayako Nishizawa-Yokoi et al.   PLANT AND CELL PHYSIOLOGY

Salt Stress Causes Peroxisome Proliferation, but Inducing Peroxisome Proliferation Does Not Improve NaCl Tolerance in Arabidopsis thaliana

(2010) Shiro Mitsuya et al.   PLoS One

Salt tolerance mechanisms in mangroves: a review

(2010) Asish Kumar Parida et al.   TREES-STRUCTURE AND FUNCTION

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

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Consequences of Climate Change on the Ecogeomorphology of Coastal Wetlands

(2009) John W. Day et al.   Estuaries and Coasts

Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis

(2009) Marek Mutwil et al.   Molecular Plant

The velocity of climate change

(2009) Scott R. Loarie et al.   NATURE

A safe operating space for humanity

(2009) Johan Rockström et al.   NATURE

Shedding light on an extremophile lifestyle through transcriptomics

(2009) M. Dassanayake et al.   NEW PHYTOLOGIST

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Peroxule extension over ER-defined paths constitutes a rapid subcellular response to hydroxyl stress

(2009) Alison M. Sinclair et al.   PLANT JOURNAL

Specific Arabidopsis HSP90.2 alleles recapitulate RAR1 cochaperone function in plant NB-LRR disease resistance protein regulation

(2009) D. A. Hubert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of sea-level and climatic changes on the Amazon coastal wetlands during the late Holocene

(2009) Marcelo Cancela Lisboa Cohen et al.   VEGETATION HISTORY AND ARCHAEOBOTANY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Environmental drivers in mangrove establishment and early development: A review

(2008) Ken W. Krauss et al.   AQUATIC BOTANY

Wetland dynamics of Marajó Island, northern Brazil, during the last 1000 years

(2008) M.C.L. Cohen et al.   CATENA

Palaeolimnological studies and ancient maps confirm secular climate fluctuations in Amazonia

(2008) Rubén J. Lara et al.   CLIMATIC CHANGE

Climatic and anthropogenic factors affecting river discharge to the global ocean, 1951–2000

(2008) J.D. Milliman et al.   GLOBAL AND PLANETARY CHANGE

ENSO and Extreme Rainfall Events in South America

(2008) Alice M. Grimm et al.   JOURNAL OF CLIMATE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Mangrove forests: Resilience, protection from tsunamis, and responses to global climate change

(2007) Daniel M. Alongi   ESTUARINE COASTAL AND SHELF SCIENCE