(Q34701539)

4 August 2017

title

Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly (English)

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4 August 2017

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Takayuki Yazawa

1

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4 August 2017

Hiroyuki Kawahigashi

series ordinal

2

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4 August 2017

Takashi Matsumoto

series ordinal

3

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4 August 2017

Hiroshi Mizuno

series ordinal

4

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4 August 2017

language of work or name

English

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publication date

30 April 2013

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4 August 2017

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4 August 2017

volume

8

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4 August 2017

issue

4

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4 August 2017

page(s)

e62460

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Creative Commons Attribution 4.0 International

4 August 2017

copyright license

start time

30 April 2013

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

1 reference

Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

CDPKs in immune and stress signaling

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The unfolded protein response in secretory cell function.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Dual RNA-seq of pathogen and host

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-interaction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Plant innate immunity: perception of conserved microbial signatures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Fast gapped-read alignment with Bowtie 2

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Phytozome: a comparative platform for green plant genomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

InterPro in 2011: new developments in the family and domain prediction database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The cross-pathway control system regulates production of the secondary metabolite toxin, sirodesmin PL, in the ascomycete, Leptosphaeria maculans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Fungal enzyme sets for plant polysaccharide degradation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Protein kinase signaling networks in plant innate immunity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

A rice calcium-dependent protein kinase is expressed in cortical root cells during the presymbiotic phase of the arbuscular mycorrhizal symbiosis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Expression of the rice CDPK-7 in sorghum: molecular and phenotypic analyses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Rice hypersensitive induced reaction protein 1 (OsHIR1) associates with plasma membrane and triggers hypersensitive cell death.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

CDD: a Conserved Domain Database for the functional annotation of proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Enhanced disease resistance in transgenic carrot (Daucus carota L.) plants over-expressing a rice cationic peroxidase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Getting the most from the host: how pathogens force plants to cooperate in disease

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Plant immunity: towards an integrated view of plant-pathogen interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

BLAST+: architecture and applications

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The Pfam protein families database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Roadmap for future research on plant pathogen effectors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Receptor-mediated signalling in plants: molecular patterns and programmes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The Sequence Alignment/Map format and SAMtools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The role of WRKY transcription factors in plant immunity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Fungal LysM effectors: extinguishers of host immunity?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

TopHat: discovering splice junctions with RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The Sorghum bicolor genome and the diversification of grasses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

A role for the unfolded protein response (UPR) in virulence and antifungal susceptibility in Aspergillus fumigatus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in Medicago truncatula

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Specific functions of individual class III peroxidase genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

A class III peroxidase specifically expressed in pathogen-attacked barley epidermis contributes to basal resistance.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

PeroxiBase: a database with new tools for peroxidase family classification

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Mapping and quantifying mammalian transcriptomes by RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Unique aspects of the grass cell wall

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

NtLRP1, a tobacco leucine-rich repeat gene with a possible role as a modulator of the hypersensitive response

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Significance of inducible defense-related proteins in infected plants.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Profiling of wheat class III peroxidase genes derived from powdery mildew-attacked epidermis reveals distinct sequence-associated expression patterns

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Differential activity of peroxidase isozymes in response to wounding, gypsy moth, and plant hormones in northern red oak (Quercus rubra L.).

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

PrediSi: prediction of signal peptides and their cleavage positions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The Aspergillus fumigatus transcriptional activator CpcA contributes significantly to the virulence of this fungal pathogen

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

BLAT—The BLAST-Like Alignment Tool

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

PLACE: a database of plant cis-acting regulatory DNA elements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Isolation of a cDNA encoding a novel leucine-rich repeat motif from Sorghum bicolor inoculated with fungi

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

A novel mechanism for regulating activity of a transcription factor that controls the unfolded protein response

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

Cross-pathway regulation: histidine-mediated control of histidine, tryptophan, and arginine biosynthetic enzymes in Neurospora crassa

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3640049

PlnTFDB: updated content and new features of the plant transcription factor database

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Woronin body function in Magnaporthe grisea is essential for efficient pathogenesis and for survival during nitrogen starvation stress

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

A novel simple extracellular leucine-rich repeat (eLRR) domain protein from rice (OsLRR1) enters the endosomal pathway and interacts with the hypersensitive-induced reaction protein 1 (OsHIR1).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Proteomic analysis of rice plasma membrane reveals proteins involved in early defense response to bacterial blight

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

The hypersensitive induced reaction and leucine-rich repeat proteins regulate plant cell death associated with disease and plant immunity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

The class III peroxidase multigenic family in rice and its evolution in land plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Rice cationic peroxidase accumulates in xylem vessels during incompatible interactions with Xanthomonas oryzae pv oryzae

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Vascular defense responses in rice: peroxidase accumulation in xylem parenchyma cells and xylem wall thickening

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Stable expression of a defense-related gene in wheat epidermis under transcriptional control of a novel promoter confers pathogen resistance

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Tissue-specific expression of a defence-related peroxidase in transgenic wheat potentiates cell death in pathogen-attacked leaf epidermis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Signal-3L: A 3-layer approach for predicting signal peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Confidence Limits on Phylogenies: an Approach using the Bootstrap

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0062460

Positional cloning of ds1, the target leaf spot resistance gene against Bipolaris sorghicola in sorghum

21 January 2018

1 reference

12 December 2020

Increased Activity of a Cationic Peroxidase Associated with an Incompatible Interaction Between Xanthomonas oryzae pv oryzae and Rice (Oryza sativa)

1 reference

12 December 2020

Over-expression of rice leucine-rich repeat protein results in activation of defense response, thereby enhancing resistance to bacterial soft rot in Chinese cabbage

1 reference

12 December 2020

Rice WRKY45 plays important roles in fungal and bacterial disease resistance

1 reference

12 December 2020

Analysis of transcriptome changes induced by Ptr ToxA in wheat provides insights into the mechanisms of plant susceptibility

1 reference

12 December 2020

Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0062460

Identifiers

DOI

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4 August 2017

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4 August 2017

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