The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program
We developed a genome-wide transcriptomic atlas of grapevine (Vitis vinifera) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed -9 1% of the predi...
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| Veröffentlicht in: | The Plant cell 2012-09, Vol.24 (9), p.3489-3505 |
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| creator | Fasoli, Marianna Dal Santo, Silvia Zenoni, Sara Tornielli, Giovanni Battista Farina, Lorenzo Zamboni, Anita Porceddu, Andrea Venturini, Luca Bicego, Manuele Murino, Vittorio Ferrarini, Alberto Delledonne, Massimo Pezzotti, Mario |
| description | We developed a genome-wide transcriptomic atlas of grapevine (Vitis vinifera) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed -9 1% of the predicted grapevine genes. Pollen and senescent leaves had unique transcriptomes reflecting their specialized functions and physiological status. However, microarray and RNA-seq analysis grouped all the other samples into two major classes based on maturity rather than organ identity, namely, the vegetative/green and mature/woody categories. This division represents a fundamental transcriptomic reprogramming during the maturation process and was highlighted by three statistical approaches identifying the transcriptional relationships among samples (correlation analysis), putative biomarkers (O2PLS-DA approach), and sets of strongly and consistently expressed genes that define groups (topics) of similar samples (biclustering analysis). Gene coexpression analysis indicated that the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of clusters of neighboring genes and global regulation based on codon preference. This global transcriptomic reprogramming during maturation has not been observed in herbaceous annual species and may be a defining characteristic of perennial woody plants. |
| doi_str_mv | 10.1105/tpc.112.100230 |
| format | Article |
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Together, these samples expressed -9 1% of the predicted grapevine genes. Pollen and senescent leaves had unique transcriptomes reflecting their specialized functions and physiological status. However, microarray and RNA-seq analysis grouped all the other samples into two major classes based on maturity rather than organ identity, namely, the vegetative/green and mature/woody categories. This division represents a fundamental transcriptomic reprogramming during the maturation process and was highlighted by three statistical approaches identifying the transcriptional relationships among samples (correlation analysis), putative biomarkers (O2PLS-DA approach), and sets of strongly and consistently expressed genes that define groups (topics) of similar samples (biclustering analysis). Gene coexpression analysis indicated that the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of clusters of neighboring genes and global regulation based on codon preference. This global transcriptomic reprogramming during maturation has not been observed in herbaceous annual species and may be a defining characteristic of perennial woody plants.</description><identifier>ISSN: 1040-4651</identifier><identifier>EISSN: 1532-298X</identifier><identifier>DOI: 10.1105/tpc.112.100230</identifier><identifier>PMID: 22948079</identifier><language>eng</language><publisher>United States: American Society of Plant Biologists</publisher><subject>Berries ; Chromosomes, Plant - genetics ; Cluster Analysis ; Codons ; Correlations ; Datasets ; Developmental biology ; Fruit - genetics ; Fruit - growth & development ; Fruit - physiology ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant - genetics ; Genes ; Genes, Plant - genetics ; Genetic Markers ; Genome, Plant - genetics ; Genomes ; Large-Scale Biology ; LARGE-SCALE BIOLOGY ARTICLES ; Oligonucleotide Array Sequence Analysis ; Organ Specificity ; Plant cells ; Plant Leaves - genetics ; Plant Leaves - growth & development ; Plant Leaves - physiology ; Plant Stems - genetics ; Plant Stems - growth & development ; Plant Stems - physiology ; Plants ; Pollen - genetics ; Pollen - growth & development ; Pollen - physiology ; RNA, Plant - genetics ; RNA, Plant - metabolism ; Species Specificity ; Transcriptome ; Transcriptomes ; transcriptomics ; Vitis ; Vitis - genetics ; Vitis - growth & development ; Vitis - physiology</subject><ispartof>The Plant cell, 2012-09, Vol.24 (9), p.3489-3505</ispartof><rights>2012 American Society of Plant Biologists</rights><rights>2012 American Society of Plant Biologists. All rights reserved. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c445t-51d002ab1218fc46a95fcc9ba98f67dfe6220c174c5533dee694cc57c00474cb3</citedby><cites>FETCH-LOGICAL-c445t-51d002ab1218fc46a95fcc9ba98f67dfe6220c174c5533dee694cc57c00474cb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/41692821$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/41692821$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,776,780,799,881,27901,27902,57992,58225</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22948079$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fasoli, Marianna</creatorcontrib><creatorcontrib>Dal Santo, Silvia</creatorcontrib><creatorcontrib>Zenoni, Sara</creatorcontrib><creatorcontrib>Tornielli, Giovanni Battista</creatorcontrib><creatorcontrib>Farina, Lorenzo</creatorcontrib><creatorcontrib>Zamboni, Anita</creatorcontrib><creatorcontrib>Porceddu, Andrea</creatorcontrib><creatorcontrib>Venturini, Luca</creatorcontrib><creatorcontrib>Bicego, Manuele</creatorcontrib><creatorcontrib>Murino, Vittorio</creatorcontrib><creatorcontrib>Ferrarini, Alberto</creatorcontrib><creatorcontrib>Delledonne, Massimo</creatorcontrib><creatorcontrib>Pezzotti, Mario</creatorcontrib><title>The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program</title><title>The Plant cell</title><addtitle>Plant Cell</addtitle><description>We developed a genome-wide transcriptomic atlas of grapevine (Vitis vinifera) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed -9 1% of the predicted grapevine genes. Pollen and senescent leaves had unique transcriptomes reflecting their specialized functions and physiological status. However, microarray and RNA-seq analysis grouped all the other samples into two major classes based on maturity rather than organ identity, namely, the vegetative/green and mature/woody categories. This division represents a fundamental transcriptomic reprogramming during the maturation process and was highlighted by three statistical approaches identifying the transcriptional relationships among samples (correlation analysis), putative biomarkers (O2PLS-DA approach), and sets of strongly and consistently expressed genes that define groups (topics) of similar samples (biclustering analysis). Gene coexpression analysis indicated that the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of clusters of neighboring genes and global regulation based on codon preference. This global transcriptomic reprogramming during maturation has not been observed in herbaceous annual species and may be a defining characteristic of perennial woody plants.</description><subject>Berries</subject><subject>Chromosomes, Plant - genetics</subject><subject>Cluster Analysis</subject><subject>Codons</subject><subject>Correlations</subject><subject>Datasets</subject><subject>Developmental biology</subject><subject>Fruit - genetics</subject><subject>Fruit - growth & development</subject><subject>Fruit - physiology</subject><subject>Gene Expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant - genetics</subject><subject>Genes</subject><subject>Genes, Plant - genetics</subject><subject>Genetic Markers</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>Large-Scale Biology</subject><subject>LARGE-SCALE BIOLOGY ARTICLES</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Organ Specificity</subject><subject>Plant cells</subject><subject>Plant Leaves - genetics</subject><subject>Plant Leaves - growth & development</subject><subject>Plant Leaves - physiology</subject><subject>Plant Stems - genetics</subject><subject>Plant Stems - growth & development</subject><subject>Plant Stems - physiology</subject><subject>Plants</subject><subject>Pollen - genetics</subject><subject>Pollen - growth & development</subject><subject>Pollen - physiology</subject><subject>RNA, Plant - genetics</subject><subject>RNA, Plant - metabolism</subject><subject>Species Specificity</subject><subject>Transcriptome</subject><subject>Transcriptomes</subject><subject>transcriptomics</subject><subject>Vitis</subject><subject>Vitis - genetics</subject><subject>Vitis - growth & development</subject><subject>Vitis - physiology</subject><issn>1040-4651</issn><issn>1532-298X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUcFOGzEUtKqiQinX3lr52MsGP6-9u75UQpBCJRCoBImb5ThvE6Pd9dZ2Ivh7HIVG7aknj_xmRm_eEPIZ2ASAydM02gz4BBjjJXtHjkCWvOCqeXyfMROsEJWEQ_IxxifGGNSgPpBDzpVoWK2OSJqtkF4GM-LGDUinz2PAGJ0f6FnqTKS_cIOmi9TQC8SRzoIZog1uTL5Her9ybaIXwWXtkqbsNB2SC0jvOjMk6obks_DGpHUwaet5F_wymP4TOWizKZ68vcfk4cd0dn5VXN9e_jw_uy6sEDIVEhY5lZkDh6a1ojJKttaquVFNW9WLFivOmYVaWCnLcoFYKWGtrC1jIn_Oy2Pyfec7ruc9LiwOKZhOj8H1Jrxob5z-dzK4lV76jS7zdXgjssG3N4Pgf68xJt27aLHL8dCvo-bbk_KaV-y_VADIW0LFZaZOdlQbfIwB2_1GwPS2VZ1bzYDrXatZ8PXvHHv6nxoz4cuO8BSTD_u5gErxhkP5Cmi9qQI</recordid><startdate>20120901</startdate><enddate>20120901</enddate><creator>Fasoli, Marianna</creator><creator>Dal Santo, Silvia</creator><creator>Zenoni, Sara</creator><creator>Tornielli, Giovanni Battista</creator><creator>Farina, Lorenzo</creator><creator>Zamboni, Anita</creator><creator>Porceddu, Andrea</creator><creator>Venturini, Luca</creator><creator>Bicego, Manuele</creator><creator>Murino, Vittorio</creator><creator>Ferrarini, Alberto</creator><creator>Delledonne, Massimo</creator><creator>Pezzotti, Mario</creator><general>American Society of Plant Biologists</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope></search><sort><creationdate>20120901</creationdate><title>The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program</title><author>Fasoli, Marianna ; Dal Santo, Silvia ; Zenoni, Sara ; Tornielli, Giovanni Battista ; Farina, Lorenzo ; Zamboni, Anita ; Porceddu, Andrea ; Venturini, Luca ; Bicego, Manuele ; Murino, Vittorio ; Ferrarini, Alberto ; Delledonne, Massimo ; Pezzotti, Mario</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c445t-51d002ab1218fc46a95fcc9ba98f67dfe6220c174c5533dee694cc57c00474cb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Berries</topic><topic>Chromosomes, Plant - genetics</topic><topic>Cluster Analysis</topic><topic>Codons</topic><topic>Correlations</topic><topic>Datasets</topic><topic>Developmental biology</topic><topic>Fruit - genetics</topic><topic>Fruit - growth & development</topic><topic>Fruit - physiology</topic><topic>Gene Expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Plant - genetics</topic><topic>Genes</topic><topic>Genes, Plant - genetics</topic><topic>Genetic Markers</topic><topic>Genome, Plant - genetics</topic><topic>Genomes</topic><topic>Large-Scale Biology</topic><topic>LARGE-SCALE BIOLOGY ARTICLES</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Organ Specificity</topic><topic>Plant cells</topic><topic>Plant Leaves - genetics</topic><topic>Plant Leaves - growth & development</topic><topic>Plant Leaves - physiology</topic><topic>Plant Stems - genetics</topic><topic>Plant Stems - growth & development</topic><topic>Plant Stems - physiology</topic><topic>Plants</topic><topic>Pollen - genetics</topic><topic>Pollen - growth & development</topic><topic>Pollen - physiology</topic><topic>RNA, Plant - genetics</topic><topic>RNA, Plant - metabolism</topic><topic>Species Specificity</topic><topic>Transcriptome</topic><topic>Transcriptomes</topic><topic>transcriptomics</topic><topic>Vitis</topic><topic>Vitis - genetics</topic><topic>Vitis - growth & development</topic><topic>Vitis - physiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fasoli, Marianna</creatorcontrib><creatorcontrib>Dal Santo, Silvia</creatorcontrib><creatorcontrib>Zenoni, Sara</creatorcontrib><creatorcontrib>Tornielli, Giovanni Battista</creatorcontrib><creatorcontrib>Farina, Lorenzo</creatorcontrib><creatorcontrib>Zamboni, Anita</creatorcontrib><creatorcontrib>Porceddu, Andrea</creatorcontrib><creatorcontrib>Venturini, Luca</creatorcontrib><creatorcontrib>Bicego, Manuele</creatorcontrib><creatorcontrib>Murino, Vittorio</creatorcontrib><creatorcontrib>Ferrarini, Alberto</creatorcontrib><creatorcontrib>Delledonne, Massimo</creatorcontrib><creatorcontrib>Pezzotti, Mario</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The Plant cell</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fasoli, Marianna</au><au>Dal Santo, Silvia</au><au>Zenoni, Sara</au><au>Tornielli, Giovanni Battista</au><au>Farina, Lorenzo</au><au>Zamboni, Anita</au><au>Porceddu, Andrea</au><au>Venturini, Luca</au><au>Bicego, Manuele</au><au>Murino, Vittorio</au><au>Ferrarini, Alberto</au><au>Delledonne, Massimo</au><au>Pezzotti, Mario</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program</atitle><jtitle>The Plant cell</jtitle><addtitle>Plant Cell</addtitle><date>2012-09-01</date><risdate>2012</risdate><volume>24</volume><issue>9</issue><spage>3489</spage><epage>3505</epage><pages>3489-3505</pages><issn>1040-4651</issn><eissn>1532-298X</eissn><abstract>We developed a genome-wide transcriptomic atlas of grapevine (Vitis vinifera) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed -9 1% of the predicted grapevine genes. Pollen and senescent leaves had unique transcriptomes reflecting their specialized functions and physiological status. However, microarray and RNA-seq analysis grouped all the other samples into two major classes based on maturity rather than organ identity, namely, the vegetative/green and mature/woody categories. This division represents a fundamental transcriptomic reprogramming during the maturation process and was highlighted by three statistical approaches identifying the transcriptional relationships among samples (correlation analysis), putative biomarkers (O2PLS-DA approach), and sets of strongly and consistently expressed genes that define groups (topics) of similar samples (biclustering analysis). Gene coexpression analysis indicated that the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of clusters of neighboring genes and global regulation based on codon preference. This global transcriptomic reprogramming during maturation has not been observed in herbaceous annual species and may be a defining characteristic of perennial woody plants.</abstract><cop>United States</cop><pub>American Society of Plant Biologists</pub><pmid>22948079</pmid><doi>10.1105/tpc.112.100230</doi><tpages>17</tpages><oa>free_for_read</oa></addata></record> |
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| source | Jstor Complete Legacy; Oxford University Press Journals All Titles (1996-Current); MEDLINE; EZB-FREE-00999 freely available EZB journals |
| subjects | Berries Chromosomes, Plant - genetics Cluster Analysis Codons Correlations Datasets Developmental biology Fruit - genetics Fruit - growth & development Fruit - physiology Gene Expression Gene Expression Profiling Gene Expression Regulation, Plant - genetics Genes Genes, Plant - genetics Genetic Markers Genome, Plant - genetics Genomes Large-Scale Biology LARGE-SCALE BIOLOGY ARTICLES Oligonucleotide Array Sequence Analysis Organ Specificity Plant cells Plant Leaves - genetics Plant Leaves - growth & development Plant Leaves - physiology Plant Stems - genetics Plant Stems - growth & development Plant Stems - physiology Plants Pollen - genetics Pollen - growth & development Pollen - physiology RNA, Plant - genetics RNA, Plant - metabolism Species Specificity Transcriptome Transcriptomes transcriptomics Vitis Vitis - genetics Vitis - growth & development Vitis - physiology |
| title | The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program |
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