Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior  

Abstract

Integrative comparative analyses of transcript and metabolite levels from climacteric and nonclimacteric fruits can be employed to unravel the similarities and differences of the underlying regulatory processes. To this end, we conducted combined gas chromatography-mass spectrometry and heterologous microarray hybridization assays in tomato (Solanum lycopersicum; climacteric) and pepper (Capsicum chilense; nonclimacteric) fruits across development and ripening. Computational methods from multivariate and network-based analyses successfully revealed the difference between the covariance structures of the integrated data sets. Moreover, our results suggest that both fruits have similar ethylene-mediated signaling components; however, their regulation is different and may reflect altered ethylene sensitivity or regulators other than ethylene in pepper. Genes involved in ethylene biosynthesis were not induced in pepper fruits. Nevertheless, genes downstream of ethylene perception such as cell wall metabolism genes, carotenoid biosynthesis genes, and the never-ripe receptor were clearly induced in pepper as in tomato fruit. While signaling sensitivity or actual signals may differ between climacteric and nonclimacteric fruit, the evidence described here suggests that activation of a common set of ripening genes influences metabolic traits. Also, a coordinate regulation of transcripts and the accumulation of key organic acids, including malate, citrate, dehydroascorbate, and threonate, in pepper fruit were observed. Therefore, the integrated analysis allows us to uncover additional information for the comprehensive understanding of biological events relevant to metabolic regulation during climacteric and nonclimacteric fruit development.

A Transcriptomic Network Underlies Microstructural and Physiological Responses to Cadmium in Populus × canescens

“…Genes that cooperate in a shared function, for example, in response to abiotic and biotic stressors, are often expressed simultaneously (Wei et al, 2006). By investigating how transcriptomic patterns vary in concert across hundreds of microarray experiments, new insights may be gained about the roles of coordinated gene networks in plants (Wei et al, 2006;Ficklin and Feltus, 2011;Osorio et al, 2012). To check whether the differentially expressed genes were coregulated in the bark of cadmium-treated P. 3 canescens, genes with unique AGIs (Supplemental Table S3) were used as query genes in the CressExpress database version 2.0 (http://cressexpress.org/index.jsp), which has analyzed correlations between genes on 486 arrays across various experimental conditions (Wei et al, 2006).…”

“…Furthermore, about one-half of the cadmium-responsive genes formed a coexpression network, indicating that P. 3 canescens coordinates the transcriptomic regulation for heavy metal stress. Recently, coregulation networks of transcriptomes have been reported in rice , Arabidopsis (Bassel et al, 2011;Movahedi et al, 2011), pepper (Capsicum annuum), and tomato (Solanum lycopersicum; Osorio et al, 2012), and maize (Zea mays; Ficklin and Feltus, 2011). However, none of these studies have addressed the coexpression of genes in response to cadmium in plants.…”

Network Analysis of Postharvest Senescence Process in Citrus Fruits Revealed by Transcriptomic and Metabolomic Profiling

“…High-throughput molecular biological techniques like transcriptomic, proteomic, and metabolomic approaches have been widely used to explore aging-related mechanisms in fruits, as reported in tomato (Kok et al, 2008;Karlova et al, 2011;Osorio et al, 2011), pepper (Capsicum annuum; Osorio et al, 2012), grape (Fasoli et al, 2012), peach (Prunus persica; Jiang et al, 2014), apple (Zheng et al, 2013), melon (Cucumis melo; Bernillon et al, 2013), strawberry (Kang et al, 2013), and cassava (Manihot esculenta; Vanderschuren et al, 2014). The combination analysis of different omics data sets by network construction has been used to unravel the regulatory relationship or changes of metabolic pathways during the ripening and senescence process in strawberry (Fait et al, 2008), tomato (Enfissi et al, 2010;Lee et al, 2012), and peach (Lombardo et al, 2011).…”

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

“…Despite the remarkable ability of cork oak to produce cork, potato has been the preferred model to study these processes since it is more amenable to in vitro manipulation and transformation having, in addition, its genome fully sequenced (Xu et al 2011). However, it is becoming increasingly evident that species-specific regulators are crucial in the regulation of a wide range of processes including developmental processes (Osorio et al 2012 ;Sunkar et al 2007). …”