Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening

Abstract

Red wolfberry (or goji berry, Lycium barbarum; LB) is an important agricultural product with a high content of pharmacologically important secondary metabolites such as phenylpropanoids. A close relative, black wolfberry (L. ruthenicum; LR), endemic to the salinized deserts of northwestern china, is used only locally. The two fruits exhibit many morphological and phytochemical differences, but genetic mechanisms underlying them remain poorly explored. in order to identify the genes of interest for further studies, we studied transcriptomic (Illumina HiSeq) and metabolomic (LC-MS) profiles of the two fruits during five developmental stages (young to ripe). As expected, we identified much higher numbers of significantly differentially regulated genes (DEGs) than metabolites. The highest numbers were identified in pairwise comparisons including the first stage for both species, but total numbers were consistently somewhat lower for the LR. The number of differentially regulated metabolites in pairwise comparisons of developmental stages varied from 66 (stages 3 vs 4) to 133 (stages 2 vs 5) in both species. We identified a number of genes (e.g. AAT1, metE, pip) and metabolites (e.g. rutin, raffinose, galactinol, trehalose, citrulline and DL-arginine) that may be of interest to future functional studies of stress adaptation in plants. As LB is also highly suitable for combating soil desertification and alleviating soil salinity/alkalinity/pollution, its potential for human use may be much wider than its current, highly localized, relevance.Despite their close phylogenetic relationship, the fruits of these two species exhibit distinct phenotypic profiles of during all developmental stages, including their shape, size, colour, taste, nutritional value and pharmacological properties 3,4,11 . As opposed to the red and elongated mature red wolfberry, black wolfberry is dark-purple or black, round, and smaller. It is also known that metabolic phenotypes of these two fruits differ significantly, particularly in the content of fatty acids, phenols and antioxidant capacities, which are much higher in black wolfberry, while the content of carotenoids, sugars, amino acids and osmolytes is higher in the red wolfberry 3,4 .Fruit ripening is a complex developmental process, coordinated by a network of interacting genes and signalling pathways 12 , so genetic mechanisms underpinning these phenotypic differences remain only partially understood. The objective of this study was to contribute to our understanding of the complexity of ripening processes of these two fruits in different environments. To achieve this, we collected L. barbarum and L. ruthenicum fruits at five developmental stages, from young to ripe fruit, and sequenced their transcriptomes and metabolomes. These data shall help us better understand genetic underpinnings of both within-and between-species phenotypic differences that fruits of these two species exhibit during their respective ripening processes. Materials and methodsSample collection. Fruits were collected ...

Metabolomics and Transcriptomics Analyses Reveal Regulatory Networks Associated with Fatty Acid Accumulation in Pecan Kernels

“…ABI3 might activate FA synthesis by upregulating the expression levels of 20 lipid droplet protein genes ( oleosins and caleosins ) and WRI1 . Therefore, the functions of LEC1 , FUS3 , and ABI3 might mediate FA synthesis by regulating the transcription of WRI1 in pecan nuts …”

“…Zhang et al demonstrated that flavonoids, particularly anthocyanins, were the major components that modulated jujube peel reddening and further obtained three UDP-glucose flavonoid 3-O-glucosyltransferase genes implicated in the extensive accumulation of anthocyanins . Moreover, similar studies were performed in Lycium ruthenicum , L. barbarum , Actinidia arguta , bamboo, and pepper . Nevertheless, the dynamic changes in metabolomics during pecan nut development and its molecular regulation mechanisms are yet to be reported.…”

Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns

“…EP genes were selected manually in a way to select genes with the expression peaking in each of the five developmental stages. MS category of genes was identified for each species in a previous study by overlapping the sets of differentially expressed genes and metabolites [22]. To annotate the identified ADT paralogues as reliably as possible, we conducted phylogenetic analyses using PHYLOSUITE [28] and its plug-in programmes.…”

“…Their metabolic profiles also differ significantly, particularly in the content of fatty acids, phenols and antioxidant capacities, which are much higher in LR, while the content of carotenoids, sugars, amino acids and osmolytes is higher in LB [6,8,9]. Although several studies have reported transcriptomic profiles of LB and/or LR fruits [7, 21,22], fruit ripening is a complex developmental process, coordinated by a network of interacting genes and signalling pathways, and the genetic mechanisms underpinning these phenotypic differences remain only partially understood [6, [23][24][25][26]. Therefore, the objective of our study was to study expression patterns of genes that may have major contributions to these phenotypic differences and identify individual genes that may have unique functions in any of these two species, and therefore warrant further studies.…”

Integrated Metabolomic and Transcriptomic Analysis Reveals Differential Flavonoid Accumulation and Its Underlying Mechanism in Fruits of Distinct Canarium album Cultivars

“…The metabolomics technology is a powerful tool that can be used to explore the differences in composition and content of metabolic components in different samples, and to clarify the mechanism underlying certain phenomena, such as fruit quality formation, biotic/abiotic stress responses, variety specificity, and so on [ 20 ]. Using an integrated analysis of the transcriptome and metabolome, Zhao et al revealed the changes in the accumulation of metabolites and the expression of metabolites biosynthesis-related genes during fruit ripening of Lycium ruthenicum and L. barbarum , and laid a foundation for the exploration of genetic color variation mechanisms [ 21 ]. Jia et al explored the key genes regulating white petal color in Brassica napus and provided important insights into the molecular mechanisms of the carotenoid metabolism pathway associated with color variations in rapeseed petals [ 22 ].…”