Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck).
Identifieur interne : 000054 ( PubMed/Corpus ); précédent : 000053; suivant : 000055Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck).
Auteurs : Dingquan Huang ; Yihong Zhao ; Minghao Cao ; Liang Qiao ; Zhi-Liang ZhengSource :
- Frontiers in plant science ; 2016.
Abstract
Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control.
DOI: 10.3389/fpls.2016.00486
PubMed: 27092171
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Osbeck).</title><author><name sortKey="Huang, Dingquan" sort="Huang, Dingquan" uniqKey="Huang D" first="Dingquan" last="Huang">Dingquan Huang</name><affiliation><nlm:affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhao, Yihong" sort="Zhao, Yihong" uniqKey="Zhao Y" first="Yihong" last="Zhao">Yihong Zhao</name><affiliation><nlm:affiliation>Division of Biostatistics, Department of Child Psychiatry, New York University Langone Medical Center, New York NY, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Cao, Minghao" sort="Cao, Minghao" uniqKey="Cao M" first="Minghao" last="Cao">Minghao Cao</name><affiliation><nlm:affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Qiao, Liang" sort="Qiao, Liang" uniqKey="Qiao L" first="Liang" last="Qiao">Liang Qiao</name><affiliation><nlm:affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Zhi Liang" sort="Zheng, Zhi Liang" uniqKey="Zheng Z" first="Zhi-Liang" last="Zheng">Zhi-Liang Zheng</name><affiliation><nlm:affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China; Department of Biological Sciences, Lehman College, City University of New York, BronxNY, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27092171</idno><idno type="pmid">27092171</idno><idno type="doi">10.3389/fpls.2016.00486</idno><idno type="wicri:Area/PubMed/Corpus">000054</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck).</title><author><name sortKey="Huang, Dingquan" sort="Huang, Dingquan" uniqKey="Huang D" first="Dingquan" last="Huang">Dingquan Huang</name><affiliation><nlm:affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhao, Yihong" sort="Zhao, Yihong" uniqKey="Zhao Y" first="Yihong" last="Zhao">Yihong Zhao</name><affiliation><nlm:affiliation>Division of Biostatistics, Department of Child Psychiatry, New York University Langone Medical Center, New York NY, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Cao, Minghao" sort="Cao, Minghao" uniqKey="Cao M" first="Minghao" last="Cao">Minghao Cao</name><affiliation><nlm:affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Qiao, Liang" sort="Qiao, Liang" uniqKey="Qiao L" first="Liang" last="Qiao">Liang Qiao</name><affiliation><nlm:affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zheng, Zhi Liang" sort="Zheng, Zhi Liang" uniqKey="Zheng Z" first="Zhi-Liang" last="Zheng">Zhi-Liang Zheng</name><affiliation><nlm:affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China; Department of Biological Sciences, Lehman College, City University of New York, BronxNY, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27092171</PMID><DateCreated><Year>2016</Year><Month>4</Month><Day>19</Day></DateCreated><DateCompleted><Year>2016</Year><Month>04</Month><Day>19</Day></DateCompleted><DateRevised><Year>2016</Year><Month>4</Month><Day>21</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck).</ArticleTitle><Pagination><MedlinePgn>486</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2016.00486</ELocationID><Abstract><AbstractText>Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Dingquan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Yihong</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Division of Biostatistics, Department of Child Psychiatry, New York University Langone Medical Center, New York NY, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Minghao</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qiao</LastName><ForeName>Liang</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest University Chongqing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Zhi-Liang</ForeName><Initials>ZL</Initials><AffiliationInfo><Affiliation>Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China; Department of Biological Sciences, Lehman College, City University of New York, BronxNY, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>Apr</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><OtherID Source="NLM">PMC4824782</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Citrus</Keyword><Keyword MajorTopicYN="N">acidity</Keyword><Keyword MajorTopicYN="N">citrate</Keyword><Keyword MajorTopicYN="N">fruit</Keyword><Keyword MajorTopicYN="N">gene networks</Keyword><Keyword MajorTopicYN="N">orange</Keyword><Keyword MajorTopicYN="N">transcriptome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>11</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>3</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27092171</ArticleId><ArticleId IdType="doi">10.3389/fpls.2016.00486</ArticleId><ArticleId IdType="pmc">PMC4824782</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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