title: The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program.
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 ∼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.
authors.affiliation: Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy.
authors.forename: Marianna
authors.initials: M
authors.lastname: Fasoli
authors.forename: Silvia
authors.initials: S
authors.lastname: Dal Santo
authors.forename: Sara
authors.initials: S
authors.lastname: Zenoni
authors.forename: Giovanni Battista
authors.initials: GB
authors.lastname: Tornielli
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Farina
authors.forename: Anita
authors.initials: A
authors.lastname: Zamboni
authors.forename: Andrea
authors.initials: A
authors.lastname: Porceddu
authors.forename: Luca
authors.initials: L
authors.lastname: Venturini
authors.forename: Manuele
authors.initials: M
authors.lastname: Bicego
authors.forename: Vittorio
authors.initials: V
authors.lastname: Murino
authors.forename: Alberto
authors.initials: A
authors.lastname: Ferrarini
authors.forename: Massimo
authors.initials: M
authors.lastname: Delledonne
authors.forename: Mario
authors.initials: M
authors.lastname: Pezzotti
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D005638:Fruit / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D015870:Gene Expression; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D018547:Plant Stems / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D011058:Pollen / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity; D059467:Transcriptome; D027843:Vitis / Q000235:genetics* / Q000254:growth & development / Q000502:physiology
chemical_list: D005819:Genetic Markers; D018749:RNA, Plant