Journal
PLANT CELL
Volume 24, Issue 9, Pages 3489-3505Publisher
AMER SOC PLANT BIOLOGISTS
DOI: 10.1105/tpc.112.100230
Keywords
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Funding
- Completamento del Centro di Genomica Funzionale Vegetale project
- CARIVERONA Bank Foundation
- Valorizzazione dei Principali Vitigni Autoctoni Italiani e dei loro Terroir (Vigneto) project
- Italian Ministry of Agricultural and Forestry Policies
- Valorizzazione della tipicita dei vitigni autoctoni e dei vini veneti (Valvive)
- Regione Veneto
- Pasqua Vigneti e Cantine SpA
- Biotechnology Department of University of Verona
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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; similar to 91% 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.
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