Analysis of de novo sequencing and transcriptome assembly and lignocellulolytic enzymes gene expression of Coriolopsis gallica HTC.
Identifieur interne : 001550 ( Main/Corpus ); précédent : 001549; suivant : 001551Analysis of de novo sequencing and transcriptome assembly and lignocellulolytic enzymes gene expression of Coriolopsis gallica HTC.
Auteurs : Yuehong Chen ; Qinghua Cao ; Xiang Tao ; Huanhuan Shao ; Kun Zhang ; Yizheng Zhang ; Xuemei TanSource :
- Bioscience, biotechnology, and biochemistry [ 1347-6947 ] ; 2017.
English descriptors
- KwdEn :
- Coriolaceae (enzymology), Coriolaceae (genetics), Enzymes (genetics), Enzymes (metabolism), Fungal Proteins (genetics), Fungal Proteins (metabolism), Gene Expression Profiling (methods), Gene Expression Regulation, Fungal (MeSH), Gene Ontology (MeSH), High-Throughput Nucleotide Sequencing (methods), Lignin (genetics), Lignin (metabolism), Open Reading Frames (MeSH), Real-Time Polymerase Chain Reaction (MeSH), Transcriptome (MeSH).
- MESH :
- chemical , genetics : Enzymes, Fungal Proteins, Lignin.
- enzymology : Coriolaceae.
- genetics : Coriolaceae.
- chemical , metabolism : Enzymes, Fungal Proteins, Lignin.
- methods : Gene Expression Profiling, High-Throughput Nucleotide Sequencing.
- Gene Expression Regulation, Fungal, Gene Ontology, Open Reading Frames, Real-Time Polymerase Chain Reaction, Transcriptome.
Abstract
White-rot basidiomycete Coriolopsis gallica HTC is one of the main biodegraders of poplar. In our previous study, we have shown the strong capacity of C. gallica HTC to degrade lignocellulose. In this study, equal amounts of total RNA fromC. Gallica HTC cultures grown in different conditions were pooled together. Illumina paired-end RNA sequencing was performed, and 13.2 million 90-bp paired-end reads were generated. We chose the Merged Assembly of Oases data-set for the following blast searches and gene ontology analyses. The reads were assembled de novo into 28,034 transcripts (≥ 100 bp) using combined assembly strategy MAO. The transcripts were annotated using Blast2GO. In all, 18,810 transcripts (≥100 bp) achieved BLASTX hits, of which, 7048 transcripts had GO term and 2074 had ECs. The expression level of 11 lignocellulolytic enzyme genes from the assembled C. gallica HTC transcriptome were detected by real-time quantitative polymerase chain reaction. The results showed that expression levels of these genes were affected by carbon source and nitrogen source at the level of transcription. The current abundant transcriptome data allowed the identification of many new transcripts in C. gallica HTC. Data provided here represent the most comprehensive and integrated genomic resources for cloning and identifying genes of interest from C. gallica HTC. Characterization of C. gallica HTC transcriptome provides an effective tool to understand mechanisms underlying cellular and molecular functions of C. gallica HTC.
DOI: 10.1080/09168451.2016.1182418
PubMed: 27875934
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pubmed:27875934Le document en format XML
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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>b Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.</nlm:affiliation></affiliation></author><author><name sortKey="Shao, Huanhuan" sort="Shao, Huanhuan" uniqKey="Shao H" first="Huanhuan" last="Shao">Huanhuan Shao</name><affiliation><nlm:affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Kun" sort="Zhang, Kun" uniqKey="Zhang K" first="Kun" last="Zhang">Kun Zhang</name><affiliation><nlm:affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and 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sort="Cao, Qinghua" uniqKey="Cao Q" first="Qinghua" last="Cao">Qinghua Cao</name><affiliation><nlm:affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , 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>b Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.</nlm:affiliation></affiliation></author><author><name sortKey="Shao, Huanhuan" sort="Shao, Huanhuan" uniqKey="Shao H" first="Huanhuan" last="Shao">Huanhuan Shao</name><affiliation><nlm:affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Kun" sort="Zhang, Kun" uniqKey="Zhang K" first="Kun" last="Zhang">Kun Zhang</name><affiliation><nlm:affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , 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>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</nlm:affiliation></affiliation></author><author><name sortKey="Tan, Xuemei" sort="Tan, Xuemei" uniqKey="Tan X" first="Xuemei" last="Tan">Xuemei Tan</name><affiliation><nlm:affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Bioscience, biotechnology, and biochemistry</title><idno type="eISSN">1347-6947</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Coriolaceae (enzymology)</term><term>Coriolaceae (genetics)</term><term>Enzymes (genetics)</term><term>Enzymes (metabolism)</term><term>Fungal Proteins (genetics)</term><term>Fungal Proteins (metabolism)</term><term>Gene Expression Profiling (methods)</term><term>Gene Expression Regulation, Fungal (MeSH)</term><term>Gene Ontology (MeSH)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Lignin (genetics)</term><term>Lignin (metabolism)</term><term>Open Reading Frames (MeSH)</term><term>Real-Time Polymerase Chain Reaction (MeSH)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Enzymes</term><term>Fungal Proteins</term><term>Lignin</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Coriolaceae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coriolaceae</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Enzymes</term><term>Fungal Proteins</term><term>Lignin</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Fungal</term><term>Gene Ontology</term><term>Open Reading Frames</term><term>Real-Time Polymerase Chain Reaction</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">White-rot basidiomycete Coriolopsis gallica HTC is one of the main biodegraders of poplar. In our previous study, we have shown the strong capacity of C. gallica HTC to degrade lignocellulose. In this study, equal amounts of total RNA fromC. Gallica HTC cultures grown in different conditions were pooled together. Illumina paired-end RNA sequencing was performed, and 13.2 million 90-bp paired-end reads were generated. We chose the Merged Assembly of Oases data-set for the following blast searches and gene ontology analyses. The reads were assembled de novo into 28,034 transcripts (≥ 100 bp) using combined assembly strategy MAO. The transcripts were annotated using Blast2GO. In all, 18,810 transcripts (≥100 bp) achieved BLASTX hits, of which, 7048 transcripts had GO term and 2074 had ECs. The expression level of 11 lignocellulolytic enzyme genes from the assembled C. gallica HTC transcriptome were detected by real-time quantitative polymerase chain reaction. The results showed that expression levels of these genes were affected by carbon source and nitrogen source at the level of transcription. The current abundant transcriptome data allowed the identification of many new transcripts in C. gallica HTC. Data provided here represent the most comprehensive and integrated genomic resources for cloning and identifying genes of interest from C. gallica HTC. Characterization of C. gallica HTC transcriptome provides an effective tool to understand mechanisms underlying cellular and molecular functions of C. gallica HTC.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27875934</PMID><DateCompleted><Year>2017</Year><Month>03</Month><Day>06</Day></DateCompleted><DateRevised><Year>2017</Year><Month>03</Month><Day>06</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1347-6947</ISSN><JournalIssue CitedMedium="Internet"><Volume>81</Volume><Issue>3</Issue><PubDate><Year>2017</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Bioscience, biotechnology, and biochemistry</Title><ISOAbbreviation>Biosci Biotechnol Biochem</ISOAbbreviation></Journal><ArticleTitle>Analysis of de novo sequencing and transcriptome assembly and lignocellulolytic enzymes gene expression of Coriolopsis gallica HTC.</ArticleTitle><Pagination><MedlinePgn>460-468</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/09168451.2016.1182418</ELocationID><Abstract><AbstractText>White-rot basidiomycete Coriolopsis gallica HTC is one of the main biodegraders of poplar. In our previous study, we have shown the strong capacity of C. gallica HTC to degrade lignocellulose. In this study, equal amounts of total RNA fromC. Gallica HTC cultures grown in different conditions were pooled together. Illumina paired-end RNA sequencing was performed, and 13.2 million 90-bp paired-end reads were generated. We chose the Merged Assembly of Oases data-set for the following blast searches and gene ontology analyses. The reads were assembled de novo into 28,034 transcripts (≥ 100 bp) using combined assembly strategy MAO. The transcripts were annotated using Blast2GO. In all, 18,810 transcripts (≥100 bp) achieved BLASTX hits, of which, 7048 transcripts had GO term and 2074 had ECs. The expression level of 11 lignocellulolytic enzyme genes from the assembled C. gallica HTC transcriptome were detected by real-time quantitative polymerase chain reaction. The results showed that expression levels of these genes were affected by carbon source and nitrogen source at the level of transcription. The current abundant transcriptome data allowed the identification of many new transcripts in C. gallica HTC. Data provided here represent the most comprehensive and integrated genomic resources for cloning and identifying genes of interest from C. gallica HTC. Characterization of C. gallica HTC transcriptome provides an effective tool to understand mechanisms underlying cellular and molecular functions of C. gallica HTC.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Yuehong</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Qinghua</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tao</LastName><ForeName>Xiang</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>b Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , Sichuan , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shao</LastName><ForeName>Huanhuan</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Kun</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yizheng</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tan</LastName><ForeName>Xuemei</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>a The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology , College of Life Sciences, Sichuan University , Chengdu , China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>11</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Biosci Biotechnol Biochem</MedlineTA><NlmUniqueID>9205717</NlmUniqueID><ISSNLinking>0916-8451</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004798">Enzymes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>11132-73-3</RegistryNumber><NameOfSubstance UI="C036909">lignocellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D055453" MajorTopicYN="N">Coriolaceae</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004798" MajorTopicYN="N">Enzymes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015966" MajorTopicYN="Y">Gene Expression Regulation, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063990" MajorTopicYN="N">Gene Ontology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060888" MajorTopicYN="N">Real-Time Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Coriolopsis gallica HTC</Keyword><Keyword MajorTopicYN="Y">Gene annotation</Keyword><Keyword MajorTopicYN="Y">real-time quantitative PCR</Keyword><Keyword MajorTopicYN="Y">sequence assembler</Keyword><Keyword MajorTopicYN="Y">transcriptome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>11</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>3</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>11</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27875934</ArticleId><ArticleId IdType="doi">10.1080/09168451.2016.1182418</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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