Comparative Transcriptome Analysis of Genes Involved in GA-GID1-DELLA Regulatory Module in Symbiotic and Asymbiotic Seed Germination of Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae).
Identifieur interne : 001242 ( Main/Corpus ); précédent : 001241; suivant : 001243Comparative Transcriptome Analysis of Genes Involved in GA-GID1-DELLA Regulatory Module in Symbiotic and Asymbiotic Seed Germination of Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae).
Auteurs : Si-Si Liu ; Juan Chen ; Shu-Chao Li ; Xu Zeng ; Zhi-Xia Meng ; Shun-Xing GuoSource :
- International journal of molecular sciences [ 1422-0067 ] ; 2015.
English descriptors
- KwdEn :
- Databases, Genetic (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Ontology (MeSH), Gene Regulatory Networks (MeSH), Genes, Plant (MeSH), Germination (genetics), Molecular Sequence Annotation (MeSH), Mycorrhizae (MeSH), Orchidaceae (genetics), Orchidaceae (microbiology), Plant Proteins (genetics), Plant Proteins (metabolism), Seeds (genetics), Symbiosis (genetics), Transcriptome (genetics).
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Germination, Orchidaceae, Seeds, Symbiosis, Transcriptome.
- chemical , metabolism : Plant Proteins.
- microbiology : Orchidaceae.
- Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Ontology, Gene Regulatory Networks, Genes, Plant, Molecular Sequence Annotation, Mycorrhizae.
Abstract
Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae) is an endangered medicinal plant in China, also called "King Medicine". Due to lacking of sufficient nutrients in dust-like seeds, orchid species depend on mycorrhizal fungi for seed germination in the wild. As part of a conservation plan for the species, research on seed germination is necessary. However, the molecular mechanism of seed germination and underlying orchid-fungus interactions during symbiotic germination are poorly understood. In this study, Illumina HiSeq 4000 transcriptome sequencing was performed to generate a substantial sequence dataset of germinating A. roxburghii seed. A mean of 44,214,845 clean reads were obtained from each sample. 173,781 unigenes with a mean length of 653 nt were obtained. A total of 51,514 (29.64%) sequences were annotated, among these, 49 unigenes encoding proteins involved in GA-GID1-DELLA regulatory module, including 31 unigenes involved in GA metabolism pathway, 5 unigenes encoding GID1, 11 unigenes for DELLA and 2 unigenes for GID2. A total of 11,881 genes showed significant differential expression in the symbiotic germinating seed sample compared with the asymbiotic germinating seed sample, of which six were involved in the GA-GID1-DELLA regulatory module, and suggested that they might be induced or suppressed by fungi. These results will help us understand better the molecular mechanism of orchid seed germination and orchid-fungus symbiosis.
DOI: 10.3390/ijms161226224
PubMed: 26694378
PubMed Central: PMC4691166
Links to Exploration step
pubmed:26694378Le document en format XML
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(Orchidaceae).</title><author><name sortKey="Liu, Si Si" sort="Liu, Si Si" uniqKey="Liu S" first="Si-Si" last="Liu">Si-Si Liu</name><affiliation><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. liusisi274@126.com.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Juan" sort="Chen, Juan" uniqKey="Chen J" first="Juan" last="Chen">Juan Chen</name><affiliation><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. kibchenjuan@126.com.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Shu Chao" sort="Li, Shu Chao" uniqKey="Li S" first="Shu-Chao" last="Li">Shu-Chao Li</name><affiliation><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. lixiaofei1117@126.com.</nlm:affiliation></affiliation></author><author><name sortKey="Zeng, Xu" sort="Zeng, Xu" uniqKey="Zeng X" first="Xu" last="Zeng">Xu Zeng</name><affiliation><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. zengxu1986@sina.com.</nlm:affiliation></affiliation></author><author><name sortKey="Meng, Zhi Xia" sort="Meng, Zhi Xia" uniqKey="Meng Z" first="Zhi-Xia" last="Meng">Zhi-Xia Meng</name><affiliation><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. mengzhixianj@163.com.</nlm:affiliation></affiliation></author><author><name sortKey="Guo, Shun Xing" sort="Guo, Shun Xing" uniqKey="Guo S" first="Shun-Xing" last="Guo">Shun-Xing Guo</name><affiliation><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. sxguo1986@163.com.</nlm:affiliation></affiliation></author></analytic><series><title level="j">International journal of molecular sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Genetic (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Germination (genetics)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Mycorrhizae (MeSH)</term><term>Orchidaceae (genetics)</term><term>Orchidaceae (microbiology)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Seeds (genetics)</term><term>Symbiosis (genetics)</term><term>Transcriptome (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Germination</term><term>Orchidaceae</term><term>Seeds</term><term>Symbiosis</term><term>Transcriptome</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Orchidaceae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Gene Ontology</term><term>Gene Regulatory Networks</term><term>Genes, Plant</term><term>Molecular Sequence Annotation</term><term>Mycorrhizae</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae) is an endangered medicinal plant in China, also called "King Medicine". Due to lacking of sufficient nutrients in dust-like seeds, orchid species depend on mycorrhizal fungi for seed germination in the wild. As part of a conservation plan for the species, research on seed germination is necessary. However, the molecular mechanism of seed germination and underlying orchid-fungus interactions during symbiotic germination are poorly understood. In this study, Illumina HiSeq 4000 transcriptome sequencing was performed to generate a substantial sequence dataset of germinating A. roxburghii seed. A mean of 44,214,845 clean reads were obtained from each sample. 173,781 unigenes with a mean length of 653 nt were obtained. A total of 51,514 (29.64%) sequences were annotated, among these, 49 unigenes encoding proteins involved in GA-GID1-DELLA regulatory module, including 31 unigenes involved in GA metabolism pathway, 5 unigenes encoding GID1, 11 unigenes for DELLA and 2 unigenes for GID2. A total of 11,881 genes showed significant differential expression in the symbiotic germinating seed sample compared with the asymbiotic germinating seed sample, of which six were involved in the GA-GID1-DELLA regulatory module, and suggested that they might be induced or suppressed by fungi. These results will help us understand better the molecular mechanism of orchid seed germination and orchid-fungus symbiosis. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26694378</PMID><DateCompleted><Year>2016</Year><Month>10</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1422-0067</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><Issue>12</Issue><PubDate><Year>2015</Year><Month>Dec</Month><Day>18</Day></PubDate></JournalIssue><Title>International journal of molecular sciences</Title><ISOAbbreviation>Int J Mol Sci</ISOAbbreviation></Journal><ArticleTitle>Comparative Transcriptome Analysis of Genes Involved in GA-GID1-DELLA Regulatory Module in Symbiotic and Asymbiotic Seed Germination of Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae).</ArticleTitle><Pagination><MedlinePgn>30190-203</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms161226224</ELocationID><Abstract><AbstractText>Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae) is an endangered medicinal plant in China, also called "King Medicine". Due to lacking of sufficient nutrients in dust-like seeds, orchid species depend on mycorrhizal fungi for seed germination in the wild. As part of a conservation plan for the species, research on seed germination is necessary. However, the molecular mechanism of seed germination and underlying orchid-fungus interactions during symbiotic germination are poorly understood. In this study, Illumina HiSeq 4000 transcriptome sequencing was performed to generate a substantial sequence dataset of germinating A. roxburghii seed. A mean of 44,214,845 clean reads were obtained from each sample. 173,781 unigenes with a mean length of 653 nt were obtained. A total of 51,514 (29.64%) sequences were annotated, among these, 49 unigenes encoding proteins involved in GA-GID1-DELLA regulatory module, including 31 unigenes involved in GA metabolism pathway, 5 unigenes encoding GID1, 11 unigenes for DELLA and 2 unigenes for GID2. A total of 11,881 genes showed significant differential expression in the symbiotic germinating seed sample compared with the asymbiotic germinating seed sample, of which six were involved in the GA-GID1-DELLA regulatory module, and suggested that they might be induced or suppressed by fungi. These results will help us understand better the molecular mechanism of orchid seed germination and orchid-fungus symbiosis. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Si-Si</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. liusisi274@126.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. kibchenjuan@126.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Shu-Chao</ForeName><Initials>SC</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. lixiaofei1117@126.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zeng</LastName><ForeName>Xu</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. zengxu1986@sina.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meng</LastName><ForeName>Zhi-Xia</ForeName><Initials>ZX</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. mengzhixianj@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Shun-Xing</ForeName><Initials>SX</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. sxguo1986@163.com.</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>2015</Year><Month>12</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Int J Mol Sci</MedlineTA><NlmUniqueID>101092791</NlmUniqueID><ISSNLinking>1422-0067</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression 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MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012639" MajorTopicYN="N">Seeds</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013559" MajorTopicYN="N">Symbiosis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Anoectochilus roxburghii</Keyword><Keyword 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