Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources.

PubWeight™: 0.86‹?›

🔗 View Article (PMC 3793998)

Published in PLoS One on October 09, 2013

Authors

Keiichi Mochida1, Yukiko Uehara-Yamaguchi, Fuminori Takahashi, Takuhiro Yoshida, Tetsuya Sakurai, Kazuo Shinozaki

Author Affiliations

1: Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan ; Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan.

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

CAP3: A DNA sequence assembly program. Genome Res (1999) 50.04

GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics (2005) 21.04

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03

Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature (2010) 9.52

A physical, genetic and functional sequence assembly of the barley genome. Nature (2012) 7.25

Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17

Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15

Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67

High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics (1996) 4.41

The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23

Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters. Trends Plant Sci (2005) 3.93

Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol (2004) 3.46

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature (2013) 3.40

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res (2006) 2.90

Draft genome of the wheat A-genome progenitor Triticum urartu. Nature (2013) 2.86

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol (2013) 2.28

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res (2004) 2.19

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07

Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol (2011) 2.04

Sim4: a novel fission yeast kinetochore protein required for centromeric silencing and chromosome segregation. J Cell Biol (2003) 1.97

Brachypodium as a model for the grasses: today and the future. Plant Physiol (2011) 1.93

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A (2011) 1.85

Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res (2008) 1.82

Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. Genomics (2001) 1.76

Genome-wide survey and expression analysis of the plant-specific NAC transcription factor family in soybean during development and dehydration stress. DNA Res (2011) 1.55

TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol (2009) 1.48

Development of 5006 full-length CDNAs in barley: a tool for accessing cereal genomics resources. DNA Res (2009) 1.47

Solution structure of an Arabidopsis WRKY DNA binding domain. Plant Cell (2005) 1.45

Exploiting the Brachypodium Tool Box in cereal and grass research. New Phytol (2011) 1.43

Brachypodium distachyon genomics for sustainable food and fuel production. Curr Opin Biotechnol (2010) 1.35

Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol (2010) 1.33

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. Plant J (2009) 1.31

Systematic approaches to using the FOX hunting system to identify useful rice genes. Plant J (2008) 1.20

Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response. BMC Plant Biol (2007) 1.16

Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila. BMC Plant Biol (2008) 1.08

Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns. BMC Genomics (2009) 1.01

RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. Plant Cell Physiol (2010) 0.99

Full-length cDNA overexpressor gene hunting system (FOX hunting system). Methods Mol Biol (2011) 0.82

Mouse Genome Encyclopedia Project. Cold Spring Harb Symp Quant Biol (2003) 0.78

Articles by these authors

Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82

Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62

Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol (2006) 8.44

Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J (2002) 7.70

Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell (2003) 6.22

Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15

Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol (2006) 5.21

DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochem Biophys Res Commun (2002) 5.14

Nucleotide sequence database policies. Science (2002) 4.72

Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell (2004) 4.53

OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J (2003) 4.09

Important roles of drought- and cold-inducible genes for galactinol synthase in stress tolerance in Arabidopsis thaliana. Plant J (2002) 4.04

Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters. Trends Plant Sci (2005) 3.93

ABA-activated SnRK2 protein kinase is required for dehydration stress signaling in Arabidopsis. Plant Cell Physiol (2002) 3.90

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J (2008) 3.73

In planta functions of the Arabidopsis cytokinin receptor family. Proc Natl Acad Sci U S A (2004) 3.47

Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol (2003) 3.36

Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell (2006) 3.36

A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J (2004) 3.31

Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. Plant J (2004) 3.31

Abscisic acid-dependent multisite phosphorylation regulates the activity of a transcription activator AREB1. Proc Natl Acad Sci U S A (2006) 3.28

The NAC transcription factors NST1 and NST2 of Arabidopsis regulate secondary wall thickenings and are required for anther dehiscence. Plant Cell (2005) 3.28

Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis. Proc Natl Acad Sci U S A (2009) 3.28

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res (2007) 3.13

The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol Cell (2004) 3.04

ABA-mediated transcriptional regulation in response to osmotic stress in plants. J Plant Res (2011) 2.98

AREB1 is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. Plant Cell (2005) 2.97

Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J (2010) 2.94

Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc Natl Acad Sci U S A (2006) 2.92

NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis. Plant Cell (2007) 2.85

Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol (2008) 2.84

Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J (2007) 2.79

Perception and transduction of abscisic acid signals: keys to the function of the versatile plant hormone ABA. Trends Plant Sci (2007) 2.76

AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation. Plant J (2009) 2.73

Comparative genomics in salt tolerance between Arabidopsis and aRabidopsis-related halophyte salt cress using Arabidopsis microarray. Plant Physiol (2004) 2.71

AP2/ERF family transcription factors in plant abiotic stress responses. Biochim Biophys Acta (2011) 2.62

Three Arabidopsis SnRK2 protein kinases, SRK2D/SnRK2.2, SRK2E/SnRK2.6/OST1 and SRK2I/SnRK2.3, involved in ABA signaling are essential for the control of seed development and dormancy. Plant Cell Physiol (2009) 2.60

The regulatory domain of SRK2E/OST1/SnRK2.6 interacts with ABI1 and integrates abscisic acid (ABA) and osmotic stress signals controlling stomatal closure in Arabidopsis. J Biol Chem (2005) 2.59

Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct Integr Genomics (2002) 2.59

Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol Biol (2005) 2.56

Molecular basis of the core regulatory network in ABA responses: sensing, signaling and transport. Plant Cell Physiol (2010) 2.55

Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol (2005) 2.47

Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J (2003) 2.45

ABA-hypersensitive germination3 encodes a protein phosphatase 2C (AtPP2CA) that strongly regulates abscisic acid signaling during germination among Arabidopsis protein phosphatase 2Cs. Plant Physiol (2005) 2.44

Regulatory metabolic networks in drought stress responses. Curr Opin Plant Biol (2007) 2.39

Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci U S A (2003) 2.33

Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr Opin Biotechnol (2006) 2.30

Arabidopsis DREB2A-interacting proteins function as RING E3 ligases and negatively regulate plant drought stress-responsive gene expression. Plant Cell (2008) 2.29

ABA-Hypersensitive Germination1 encodes a protein phosphatase 2C, an essential component of abscisic acid signaling in Arabidopsis seed. Plant J (2007) 2.28

Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol (2004) 2.27

The mitogen-activated protein kinase cascade MKK3-MPK6 is an important part of the jasmonate signal transduction pathway in Arabidopsis. Plant Cell (2007) 2.26

NAC transcription factors in plant abiotic stress responses. Biochim Biophys Acta (2011) 2.24

PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol (2008) 2.22

Functional analysis of AHK1/ATHK1 and cytokinin receptor histidine kinases in response to abscisic acid, drought, and salt stress in Arabidopsis. Proc Natl Acad Sci U S A (2007) 2.22

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res (2004) 2.19

Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol (2008) 2.14

MEKK1 is required for MPK4 activation and regulates tissue-specific and temperature-dependent cell death in Arabidopsis. J Biol Chem (2006) 2.11

Antagonistic interaction between systemic acquired resistance and the abscisic acid-mediated abiotic stress response in Arabidopsis. Plant Cell (2008) 2.10

Three SnRK2 protein kinases are the main positive regulators of abscisic acid signaling in response to water stress in Arabidopsis. Plant Cell Physiol (2009) 2.06

Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol (2011) 2.04

Plants tolerant of high boron levels. Science (2007) 2.02

Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing. Proc Natl Acad Sci U S A (2007) 2.01

A collection of 11 800 single-copy Ds transposon insertion lines in Arabidopsis. Plant J (2004) 2.00

RARTF: database and tools for complete sets of Arabidopsis transcription factors. DNA Res (2005) 1.95

Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics. Plant J (2008) 1.91

Arabidopsis plasma membrane protein crucial for Ca2+ influx and touch sensing in roots. Proc Natl Acad Sci U S A (2007) 1.86

A combination of the Arabidopsis DREB1A gene and stress-inducible rd29A promoter improved drought- and low-temperature stress tolerance in tobacco by gene transfer. Plant Cell Physiol (2004) 1.84

ABC transporter AtABCG25 is involved in abscisic acid transport and responses. Proc Natl Acad Sci U S A (2010) 1.82

Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res (2008) 1.82

Two different novel cis-acting elements of erd1, a clpA homologous Arabidopsis gene function in induction by dehydration stress and dark-induced senescence. Plant J (2003) 1.81

Leucine-rich repeat receptor-like kinase1 is a key membrane-bound regulator of abscisic acid early signaling in Arabidopsis. Plant Cell (2005) 1.79

Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts. Plant Cell (2009) 1.78

Cytokinins: metabolism and function in plant adaptation to environmental stresses. Trends Plant Sci (2012) 1.78

Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics (2007) 1.77

Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana. Plant Cell Physiol (2008) 1.76

Molecular responses to drought, salinity and frost: common and different paths for plant protection. Curr Opin Biotechnol (2003) 1.74

SRK2C, a SNF1-related protein kinase 2, improves drought tolerance by controlling stress-responsive gene expression in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2004) 1.73

Transcriptional regulation of ABI3- and ABA-responsive genes including RD29B and RD29A in seeds, germinating embryos, and seedlings of Arabidopsis. Plant Mol Biol (2006) 1.68

TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell (2010) 1.67

Analysis of cytokinin mutants and regulation of cytokinin metabolic genes reveals important regulatory roles of cytokinins in drought, salt and abscisic acid responses, and abscisic acid biosynthesis. Plant Cell (2011) 1.66

CYP707A3, a major ABA 8'-hydroxylase involved in dehydration and rehydration response in Arabidopsis thaliana. Plant J (2006) 1.66

Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L. Plant J (2007) 1.65