Review of integrated metabolome and transcriptome analysis used for disclosing physiological mechanism in fruit crops

Abstract: With big data applied into researches on systematic biology, the high-throughput and high-ef- ficient integrated analysis of multi-omics has become the most popularhigh and new technology in the fields of fruit trees. Increasing studies have applied metabolomics and transcriptomics to analyze the physiological-genetic mechanisms and their regulations of fruit trees, bringing out many new discover- ies. Integrated analysis of metabolomics and transcriptomics could realize the co-expression analysis of differential metabolites and genes expressed in time series, and explore the causal relationship between genes and metabolites. The key metabolic pathways, genes and metabolites could be found accurately to analyze the correlation between regulation mechanisms and biomolecular functions of fruit trees, combined with various bioinformatics methods like functional annotation and metabolic pathway en- richment. The following is a summary of the successful application of integrated analysis of transcrip- tomics and metabolomics from three aspects: fruit quality formation and regulation, environmental re- sponse, and immune interaction mechanisms. Not only fruit growth, development and maturity, but also fruit flavor, gloss, texture, color, aroma and nutrition are affected by gene transcription and expression, and decomposition and synthesis of metabolite. Flavor quality of fruits is mainly associated with sugars and organic acids in carbohydrate metabolism. High-acid citrus fruit Gao-cheng (Citrus sp.) and low-ac-id citrus fruit Satsuma mandarin (Citrus unshiu Marc.) are selected for study based on metabolomics and transcriptomics, showing that the citric acid degradation of Satsuma mandarin is more active and two transport-related genes named as CitCHX and CitDIC are up-regulated during the growing period of Satsuma mandarin. The above-mentioned research shows that these genes may be involved in the bio- logical process in that citric acid is exported from the vacuole. Changes in the fruit texture can be divid- ed into some processes involved in softening and lignification. Studies based on metabonomics and tran- scriptomics indicate that peach fruit softening and fruit lignification may be caused by differentiations in phenylpropane metabolic pathways in fruits; the biosynthesis of phenylalanine to nanngenin chalcone is regulated by mRNA, which encodes chalcone synthase in peach‘Hongli’, resulting in active flavo- noid synthesis and fruit softening in‘Hongli’, while the expression of genes related to coenzyme A li- gase like Pp4CL2 and Pp4CL2 in peach‘Baili’is higher, which promotes the biosynthesis from phenyl- alanine to p-coumaric acid in fruits and activates downstream lignin biosynthesis and ethylene precur- sor synthesis and leads to fruit lignification. In general, anthocyanin biosynthesis at the transcriptional level is controlled by a complex of DNA-binding R2R3 MYB transcription factors, MYC-like basic he- lix-loop-helix (bHLH) proteins and WD40 proteins. Studies by Wang et al. based on HPLC-MS find that anthocyanin O-malonyl hexanoside plays an important role in the formation of purple phenotype in fig (Ficus carica L.); and meanwhile RNA-seq combined with phylogenetic clustering analysis and se- quence alignment shows that there may be transposon insertions in the MYB coding sequence in green fig, resulting in the inability to recruit R2R3 MYB transcription factors in MBW, which leads to down- regulation of a series of genes encoding chalcone synthase to UDP glucose-flavonoid 3-O-glycosyltrans- ferase in flavonoid biosynthesis pathway, and various anthocyanins like anthocyanin O-malonylhexo- side cannot be synthesized. Fruit during the growth, development and ripening must undergo various en- vironmental changes. Studies based on metabonomics show that cyanidin 3-glucoside and cyanidin 3- (6”-malonyl) glucoside are both significantly lower in the peel of bagged blood orange and bagged pur- ple pummelo, which confirms that light plays an important role in inducing anthocyanin biosynthesis in the peel of blood orange and purple pummelo; while the expressions of CsRuby1 and CgRuby1 are strongly inhibited by bagging treatment, and that sequence polymorphism comparison shows that antho- cyanin synthesis is regulated by cis element on Ruby1 promoter triggered by light in the peel of blood orange and purple pummelo. Complex defense mechanisms of fruit trees can be activated by microbial infection. To date, initiation of defence mechanisms against necrotrophic, biotrophic and hemi-biotro- phic pathogens has been unraveled with global transcriptional analysis, and studies combined with tran- scriptomics and metabonomics have opened new perspectives in further understanding the biological process of fruit-pathogen interaction recently. A genome-scale metabolic network (GEM) that integrated metabolome and transcriptome datasets obtained from a spontaneous mutant of‘Newhall’navel orange (Citrus sinensis Osbeck) with broad-spectrum protections against fungal pathogens indicates that jasmo- nate biosynthesis and signaling are stimulated by the fatty acid redirection of the mutant, and participate in the tolerance of pathogenic fungi. With the improvement of the resolution of metabolite detection and the completion of whole genome sequencing of more fruit trees, the dynamic changes of genetic tran- scription and metabolism are expected to be interpreted in greater details, so as to further expand the bioinformatics database and deepen the study on metabonomics and transcriptomics in the metabolic network and regulation mechanism of fruit trees, so as to lay a solid foundation for systematic biology and functional genomics in the future.