RustFungiGenomicsV1, Main, Exploration, bibRecordById, pubmed:26640944

Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.

Identifieur interne : 000442 ( Main/Exploration ); précédent : 000441; suivant : 000443

Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.

Auteurs : Bin He [République populaire de Chine] ; Xiang Tao [République populaire de Chine] ; Yinghong Gu [République populaire de Chine] ; Changhe Wei [République populaire de Chine] ; Xiaojie Cheng [République populaire de Chine] ; Suqin Xiao [République populaire de Chine] ; Zaiquan Cheng [République populaire de Chine] ; Yizheng Zhang [République populaire de Chine]

Source :

PloS one [ 1932-6203 ] ; 2015.

RBID : pubmed:26640944

Descripteurs français

KwdFr :
- ADN des plantes (génétique), Analyse de profil d'expression de gènes (MeSH), Analyse de séquence d'ADN (MeSH), Feuilles de plante (génétique), Maladies des plantes (microbiologie), Maladies des plantes (parasitologie), Maladies des plantes (virologie), Oryza (génétique), Racines de plante (génétique), Régulation de l'expression des gènes végétaux (MeSH), Résistance à la maladie (génétique), Séquence nucléotidique (MeSH), Tiges de plante (génétique).
MESH :
- génétique : ADN des plantes, Feuilles de plante, Oryza, Racines de plante, Résistance à la maladie, Tiges de plante.
- microbiologie : Maladies des plantes.
- parasitologie : Maladies des plantes.
- virologie : Maladies des plantes.
- Analyse de profil d'expression de gènes, Analyse de séquence d'ADN, Régulation de l'expression des gènes végétaux, Séquence nucléotidique.

English descriptors

KwdEn :
- Base Sequence (MeSH), DNA, Plant (genetics), Disease Resistance (genetics), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Oryza (genetics), Plant Diseases (microbiology), Plant Diseases (parasitology), Plant Diseases (virology), Plant Leaves (genetics), Plant Roots (genetics), Plant Stems (genetics), Sequence Analysis, DNA (MeSH).
MESH :
- chemical , genetics : DNA, Plant.
- genetics : Disease Resistance, Oryza, Plant Leaves, Plant Roots, Plant Stems.
- microbiology : Plant Diseases.
- parasitology : Plant Diseases.
- virology : Plant Diseases.
- Base Sequence, Gene Expression Profiling, Gene Expression Regulation, Plant, Sequence Analysis, DNA.

Abstract

Oryza meyeriana (O. meyeriana), with a GG genome type (2n = 24), accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. It is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq and obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (japonica-type Nipponbare and indica-type 93-11) genomes revealed that 13% of the O. meyeriana contigs had not been detected in O. sativa. Many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. There are two kinds of rice bacterial blight-resistant genes (Xa1 and Xa26) differentially or specifically expressed in O. meyeriana. The 4 Xa1 contigs were all only expressed in root, while three of Xa26 contigs have the highest expression level in leaves, two of Xa26 contigs have the highest expression profile in stems and one of Xa26 contigs was expressed dominantly in roots. The transcriptomic database of O. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease resistance in O. meyeriana.

DOI: 10.1371/journal.pone.0144518
PubMed: 26640944
PubMed Central: PMC4671656

Affiliations:

République populaire de Chine

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Le document en format XML

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<term>Disease Resistance (genetics)</term>
<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Oryza (genetics)</term>
<term>Plant Diseases (microbiology)</term>
<term>Plant Diseases (parasitology)</term>
<term>Plant Diseases (virology)</term>
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<term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Analyse de séquence d'ADN (MeSH)</term>
<term>Feuilles de plante (génétique)</term>
<term>Maladies des plantes (microbiologie)</term>
<term>Maladies des plantes (parasitologie)</term>
<term>Maladies des plantes (virologie)</term>
<term>Oryza (génétique)</term>
<term>Racines de plante (génétique)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Résistance à la maladie (génétique)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>Tiges de plante (génétique)</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Disease Resistance</term>
<term>Oryza</term>
<term>Plant Leaves</term>
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<term>Racines de plante</term>
<term>Résistance à la maladie</term>
<term>Tiges de plante</term>
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<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term>
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<front><div type="abstract" xml:lang="en">Oryza meyeriana (O. meyeriana), with a GG genome type (2n = 24), accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. It is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq and obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (japonica-type Nipponbare and indica-type 93-11) genomes revealed that 13% of the O. meyeriana contigs had not been detected in O. sativa. Many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. There are two kinds of rice bacterial blight-resistant genes (Xa1 and Xa26) differentially or specifically expressed in O. meyeriana. The 4 Xa1 contigs were all only expressed in root, while three of Xa26 contigs have the highest expression level in leaves, two of Xa26 contigs have the highest expression profile in stems and one of Xa26 contigs was expressed dominantly in roots. The transcriptomic database of O. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease resistance in O. meyeriana. </div>
</front>
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<DateCompleted><Year>2016</Year>
<Month>06</Month>
<Day>30</Day>
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<Abstract><AbstractText>Oryza meyeriana (O. meyeriana), with a GG genome type (2n = 24), accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. It is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq and obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (japonica-type Nipponbare and indica-type 93-11) genomes revealed that 13% of the O. meyeriana contigs had not been detected in O. sativa. Many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. There are two kinds of rice bacterial blight-resistant genes (Xa1 and Xa26) differentially or specifically expressed in O. meyeriana. The 4 Xa1 contigs were all only expressed in root, while three of Xa26 contigs have the highest expression level in leaves, two of Xa26 contigs have the highest expression profile in stems and one of Xa26 contigs was expressed dominantly in roots. The transcriptomic database of O. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease resistance in O. meyeriana. </AbstractText>
</Abstract>
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<Initials>B</Initials>
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<Author ValidYN="Y"><LastName>Tao</LastName>
<ForeName>Xiang</ForeName>
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<Author ValidYN="Y"><LastName>Gu</LastName>
<ForeName>Yinghong</ForeName>
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<ForeName>Changhe</ForeName>
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<ReferenceList><Reference><Citation>Nature. 2012 Oct 25;490(7421):497-501</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23034647</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Gigascience. 2012 Dec 27;1(1):18</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23587118</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Plant Mol Biol. 2007 Jul;64(5):539-47</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17530419</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 1997 Aug 22;277(5329):1063-6</Citation>
<ArticleIdList><ArticleId IdType="pubmed">9262467</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Plant Mol Biol. 2006 Jan;60(1):69-85</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16463100</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Plant Cell. 1996 May;8(5):793-803</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12239401</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2010 Jan 1;26(1):139-40</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19910308</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Theor Appl Genet. 2009 Nov;119(7):1237-46</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19669727</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 2001 Jun 14;411(6839):857-64</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11459070</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2010;11:705</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21159186</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2012 Apr 15;28(8):1086-92</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22368243</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>DNA Res. 2008 Oct;15(5):285-95</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18687674</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genetics. 2000 Apr;154(4):1819-25</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10747072</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Plant Cell Rep. 2004 Mar;22(8):569-75</Citation>
<ArticleIdList><ArticleId IdType="pubmed">14595515</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 2002 Apr 5;296(5565):92-100</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11935018</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Biol. 2010;11(10):R106</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20979621</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Rev Genet. 2010 Jan;11(1):31-46</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19997069</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2014 Jan 1;30(1):40-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24130309</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Immunol. 2005 Oct;6(10):973-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16177805</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Theor Appl Genet. 2002 Nov;105(6-7):841-846</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12582908</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 2006 Nov 16;444(7117):323-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17108957</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Protoc. 2013 Aug;8(8):1494-512</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23845962</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Annu Rev Phytopathol. 2005;43:205-27</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16078883</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Rev Immunol. 2012 Feb;12(2):89-100</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22273771</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Cell Mol Biol Lett. 2011 Mar;16(1):1-24</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20585889</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2012;13:341</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22827831</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 2004 Apr 15;428(6984):764-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15085136</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2016 Jan 4;44(D1):D457-62</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26476454</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14400-5</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10588717</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18077471</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 2005 Aug 11;436(7052):793-800</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16100779</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Cell. 2006 Feb 24;124(4):803-14</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16497589</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Trends Plant Sci. 2005 Jul;10(7):339-46</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15953753</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Res. 2010 Oct;20(10):1432-40</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20693479</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Annu Rev Phytopathol. 2001;39:285-312</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11701867</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2015;16:65</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25759274</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Biol. 2008;9(3):R49</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18315873</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Methods. 2012 Apr;9(4):357-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22388286</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Exp Bot. 2007;58(15-16):4019-26</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18182420</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Plant Cell Rep. 2004 Jun;22(11):839-47</Citation>
<ArticleIdList><ArticleId IdType="pubmed">14968263</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Res. 2006 Oct;16(10):1262-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16963705</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Exp Bot. 2012 Jun;63(11):3989-98</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22553288</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
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Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.

Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.

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