High‐spatiotemporal‐resolution transcriptomes provide insights into fruit development and ripening in Citrus sinensis

Abstract

Citrus fruit has a unique structure with soft leathery peel and pulp containing vascular bundles and several segments with many juice sacs. The function and morphology of each fruit tissue are different. Therefore, analysis at the organ-wide or mixed-tissue level inevitably obscures many tissue-specific phenomena. High-throughput RNA sequencing was used to profile Citrus sinensis fruit development based on four fruit tissue types and six development stages from young fruits to ripe fruits. Using a coexpression network analysis, modules of coexpressed genes and hub genes of tissue-specific networks were identified. Of particular, importance is the discovery of the regulatory network of phytohormones during citrus fruit development and ripening. A model was proposed to illustrate how ABF2 mediates the ABA signalling involved in sucrose transport, chlorophyll degradation, auxin homoeostasis, carotenoid and ABA biosynthesis, and cell wall metabolism during citrus fruit development. Moreover, we depicted the detailed spatiotemporal expression patterns of the genes involved in sucrose and citric acid metabolism in citrus fruit and identified several key genes that may play crucial roles in sucrose and citric acid accumulation in the juice sac, such as SWEET15 and CsPH8. The high spatial and temporal resolution of our data provides important insights into the molecular networks underlying citrus fruit development and ripening.

Metabolomic and transcriptomic analyses reveal the mechanism of sweet-acidic taste formation during pineapple fruit development

“…In the present study, the SUT gene (Aco000269) expression level showing a positive correlation with Suc content suggested that it was involved in apoplast unloading of Suc, whereas the SUT gene (Aco004135) expression level displaying a negative correlation with Suc content suggested that it was involved in Suc efflux from the vacuole membrane to the cytoplasm. Furthermore, the positive correlation between the SWEET gene (Aco016508) expression level and Suc content in this study showed that it might mediate Suc release into the apoplast and contribute to Suc accumulation in pineapple fruit based on a study in Citrus (Feng et al, 2021). The expression levels of the other three SWEET genes were negatively correlated with Suc content, which was consistent with previous studies (Guo et al, 2018).…”

“…Citrate degradation by the GABA pathway in the cytosol is also a key player in fruit acidity ( Batista-Silva et al, 2018 ). GADs catalyze the decarboxylation of glutamate to GABA and are related to citrate accumulation, and the higher expression of GAD genes contribute to the decrease in fruit acidity at the late stage of development ( Liu et al, 2014 ; Feng et al, 2021 ). Low-acid cultivars exhibited citrate degradation attributed to the upregulation of GAD gene expression in peach ( Zheng et al, 2020 ).…”

Comparative Analysis of the Chalcone-Flavanone Isomerase Genes in Six Citrus Species and Their Expression Analysis in Sweet Orange (Citrus sinensis)

“…We collected the expression profiles of C. sinensis (‘Fengjie 72-1′) albedo, epicarp, juice sac, and segment membrane from six fruit development stages, including 50 days after flowering (the second physiological fruit-falling period); 80, 120, and 155 days after flowering (the expansion period); 180 days after flowering (the coloring period), and 220 days after flowering (the full-ripening period) ( Feng et al, 2021 ). The average expression of all CsCHI genes was the highest in the 50 DAF stage, then decreased rapidly, and increased slightly in the 155 DAF stage ( Supplementary Table S4 ).…”

“…RNA-seq data for C. sinensis were obtained from the NCBI GEO DataSets under accession numbers PRJNA689213 and PRJNA517400 ( Feng et al, 2021 ; Huang et al, 2021 ). The transcriptome data of pulp and peel contained two types of sweet oranges (Valencia orange and common sweet orange), involving six varieties.…”

“…Compared with the common sweet orange, Valencia orange belonged to late-ripening sweet oranges which had poor mastication traits ( Wu et al, 2020 ). The transcriptome data of fruit development included four tissues (albedo, epicarp, juice sac, and segment membrane), involving four periods (the second physiological fruit-falling period, the expansion period, the coloring period, and the full-ripening period), which were divided into six time points ( Feng et al, 2021 ). We extracted the expression of CHI genes and analyzed the expression pattern using the R package pheatmap.…”