Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.
Identifieur interne : 000426 ( Main/Corpus ); précédent : 000425; suivant : 000427Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.
Auteurs : Bin He ; Xiang Tao ; Yinghong Gu ; Changhe Wei ; Xiaojie Cheng ; Suqin Xiao ; Zaiquan Cheng ; Yizheng ZhangSource :
- PloS one [ 1932-6203 ] ; 2015.
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
Links to Exploration step
pubmed:26640944Le document en format XML
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of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</nlm:affiliation></affiliation></author><author><name sortKey="Tao, Xiang" sort="Tao, Xiang" uniqKey="Tao X" first="Xiang" last="Tao">Xiang Tao</name><affiliation><nlm:affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</nlm:affiliation></affiliation></author><author><name sortKey="Gu, Yinghong" sort="Gu, Yinghong" uniqKey="Gu Y" first="Yinghong" last="Gu">Yinghong Gu</name><affiliation><nlm:affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wei, Changhe" sort="Wei, Changhe" uniqKey="Wei C" first="Changhe" last="Wei">Changhe Wei</name><affiliation><nlm:affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</nlm:affiliation></affiliation></author><author><name sortKey="Cheng, Xiaojie" sort="Cheng, Xiaojie" uniqKey="Cheng X" first="Xiaojie" last="Cheng">Xiaojie Cheng</name><affiliation><nlm:affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</nlm:affiliation></affiliation></author><author><name sortKey="Xiao, Suqin" sort="Xiao, Suqin" uniqKey="Xiao S" first="Suqin" last="Xiao">Suqin Xiao</name><affiliation><nlm:affiliation>Biotechnology & Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650223, China.</nlm:affiliation></affiliation></author><author><name sortKey="Cheng, Zaiquan" sort="Cheng, Zaiquan" uniqKey="Cheng Z" first="Zaiquan" last="Cheng">Zaiquan Cheng</name><affiliation><nlm:affiliation>Biotechnology & Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650223, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Yizheng" sort="Zhang, Yizheng" uniqKey="Zhang Y" first="Yizheng" last="Zhang">Yizheng Zhang</name><affiliation><nlm:affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>DNA, Plant (genetics)</term><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><term>Plant Leaves (genetics)</term><term>Plant Roots (genetics)</term><term>Plant Stems (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Disease Resistance</term><term>Oryza</term><term>Plant Leaves</term><term>Plant Roots</term><term>Plant Stems</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Sequence Analysis, DNA</term></keywords></textClass></profileDesc></teiHeader><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></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26640944</PMID><DateCompleted><Year>2016</Year><Month>06</Month><Day>30</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>12</Issue><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Transcriptomic Analysis and the Expression of Disease-Resistant Genes in Oryza meyeriana under Native Condition.</ArticleTitle><Pagination><MedlinePgn>e0144518</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0144518</ELocationID><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><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>He</LastName><ForeName>Bin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tao</LastName><ForeName>Xiang</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gu</LastName><ForeName>Yinghong</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Changhe</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Xiaojie</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiao</LastName><ForeName>Suqin</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Biotechnology & Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650223, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Zaiquan</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Biotechnology & Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650223, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yizheng</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>12</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base 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MajorTopicYN="N">parasitology</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018547" MajorTopicYN="N">Plant Stems</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>09</Month><Day>16</Day></PubMedPubDate><PubMedPubDate 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