High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening.
Nat Commun, 2018/01/25;9(1):364.
Shinozaki Y[1], Nicolas P[2], Fernandez-Pozo N[2], Ma Q[2], Evanich DJ[2], Shi Y[2, 3], Xu Y[2], Zheng Y[2], Snyder SI[1], Martin LBB[1], Ruiz-May E[1], Thannhauser TW[4], Chen K[3], Domozych DS[5], Catalá C[1, 2], Fei Z[2, 4], Mueller LA[2], Giovannoni JJ[2, 4], Rose JKC[6]
Affiliations
PMID: 29371663DOI: 10.1038/s41467-017-02782-9
Impact factor: 17.694
Abstract
Tomato (Solanum lycopersicum) is an established model for studying fruit biology; however, most studies of tomato fruit growth and ripening are based on homogenized pericarp, and do not consider the internal tissues, or the expression signatures of individual cell and tissue types. We present a spatiotemporally resolved transcriptome analysis of tomato fruit ontogeny, using laser microdissection (LM) or hand dissection coupled with RNA-Seq analysis. Regulatory and structural gene networks, including families of transcription factors and hormone synthesis and signaling pathways, are defined across tissue and developmental spectra. The ripening program is revealed as comprising gradients of gene expression, initiating in internal tissues then radiating outward, and basipetally along a latitudinal axis. We also identify spatial variations in the patterns of epigenetic control superimposed on ripening gradients. Functional studies elucidate previously masked regulatory phenomena and relationships, including those associated with fruit quality traits, such as texture, color, aroma, and metabolite profiles.
MeSH terms
Fruit; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene Regulatory Networks; Lycopersicon esculentum; Microscopy, Electron, Transmission; Plant Proteins; Plants, Genetically Modified; Transcriptome
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