Abstract
Tomato (Solanum lycopersicum) is the primary model for the study of fleshy fruits, and research in this species has elucidated many aspects of fruit physiology, development, and metabolism. However, most of these studies have involved homogenization of the fruit pericarp, with its many constituent cell types. Here, we describe the coupling of pyrosequencing technology with laser capture microdissection to characterize the transcriptomes of the five principal tissues of the pericarp from tomato fruits (outer and inner epidermal layers, collenchyma, parenchyma, and vascular tissues) at their maximal growth phase. A total of 20,976 high-quality expressed unigenes were identified, of which more than half were ubiquitous in their expression, while others were cell type specific or showed distinct expression patterns in specific tissues. The data provide new insights into the spatial distribution of many classes of regulatory and structural genes, including those involved in energy metabolism, source-sink relationships, secondary metabolite production, cell wall biology, and cuticle biogenesis. Finally, patterns of similar gene expression between tissues led to the characterization of a cuticle on the inner surface of the pericarp, demonstrating the utility of this approach as a platform for biological discovery.
Highlights
The fleshy fruits of angiosperms have evolved complex physiologies and regulatory mechanisms to promote seed dispersal and are important components of human and animal diets
Much of what is known about fleshy fruit organogenesis, development, and maturation and the molecular bases of organoleptic and nutritional qualities has resulted from studies of tomato (Solanum lycopersicum), the principal model for fleshy fruit biology (Giovannoni, 2004; Tanksley, 2004; Paran and van der Knaap, 2007; Seymour et al, 2008; Matas et al, 2009; Klee, 2010)
Several techniques were tested to optimize the preparation of tomato fruit 10 d postanthesis (DPA; Figure 1B) pericarp samples for sectioning and laser microdissection, including fixation with acetone or ethanol:acetic acid, paraffin embedding and sectioning, or cryosectioning
Summary
The fleshy fruits of angiosperms have evolved complex physiologies and regulatory mechanisms to promote seed dispersal and are important components of human and animal diets. Research resources for tomato include linkage maps, extensive mapping and breeding germplasm collections (Gur et al, 2004; Bombarely et al, 2011), and a substantial molecular and genomic toolbox (Yano et al, 2006; Bombarely et al, 2011; Fei et al, 2011), including the release and updates of a high-quality genome sequence (http://solgenomics.net) This infrastructure has promoted major advances in the study of fruit molecular biology, physiology, and biochemistry and more recently has laid the foundation for large-scale profiling of tomato fruit transcriptomes (Alba et al, 2004, 2005; Wang et al, 2009; Osorio et al, 2011), proteomes (Faurobert et al, 2007; Yeats et al, 2010; Catalaet al., 2011), and metabolomes (Bino et al, 2005; Carrari and Fernie, 2006; Carrari et al, 2006; Nashilevitz et al, 2010). A limitation of most such studies of tomato fruit biology to date, whether examining specific phenomena or taking a nontargeted “omics” approach, is that they have mostly
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