Comparative transcriptome analysis reveals a global insight into molecular processes regulating citrate accumulation in sweet orange (Citrus sinensis)

Abstract

Citrate, the predominant organic acid in citrus, determines the taste of these fruits. However, little is known about the synergic molecular processes regulating citrate accumulation. Using 'Dahongtiancheng' (Citrus sinensis) and 'Bingtangcheng' (C. sinensis) with significant difference in citrate, the objectives of this study were to understand the global mechanisms of high-citrate accumulation in sweet orange. 'Dahongtiancheng' and 'Bingtangcheng' exhibit significantly different patterns in citrate accumulation throughout fruit development, with the largest differences observed at 50-70 days after full bloom (DAFB). Comparative transcriptome profiling was performed for the endocarps of both cultivars at 50 and 70 DAFB. Over 34.5 million clean reads per library were successfully mapped to the reference database and 670-2630 differentially expressed genes (DEGs) were found in four libraries. Among the genes, five transcription factors were ascertained to be the candidates regulating citrate accumulation. Functional assignments of the DEGs indicated that photosynthesis, the citrate cycle and amino acid metabolism were significantly altered in 'Dahongtiancheng'. Physiological and molecular analyses suggested that high photosynthetic efficiency and partial impairment of citrate catabolism were crucial for the high-citrate trait, and amino acid biosynthesis was one of the important directions for citrate flux. The results reveal a global insight into the gene expression changes in a high-citrate compared with a low-citrate sweet orange. High accumulating efficiency and impaired degradation of citrate may be associated with the high-citrate trait of 'Dahongtiancheng'. Findings in this study increase understanding of the molecular processes regulating citrate accumulation in sweet orange.

Transcriptome and Metabolome Analyses Provide Insights into the Occurrence of Peel Roughing Disorder on Satsuma Mandarin (Citrus unshiu Marc.) Fruit

“…Peels were dried at 75°C for 3 days and ground immediately in a disintegrator (FW100, TAISITE, Tianjin, China). One gram powder samples were analyzed using the published method with a HITACHIL-8900 amino acid analyser (Hitachi, Wako, Japan) (Lu et al, 2016 ). To measure the targeted starch, organic acids and sugars, the isolated and frozen CK and RD peels at 40, 80, 110, 140, and 170 DAFB were used.…”

“…The absolute amount of starch was determined by comparison with calibration standard curve and calculated based on peel fresh weight. Organic acid and sugar components were measured using high-performance liquid chromatography (HPLC) (LC-20A, Shimadzu, Kyoto, Japan) according to the published method (Lu et al, 2016 ). Organic acid and sugar were also determined in pulp using samples stored at −40°C.…”

“…Specific primers were designed from the selected gene sequences using Primer Express Version 3.0 (Applied Biosystems, CA, USA) and the primer sequences are given in Table S1 . Quantitative RT-PCR was performed according to previous reports (Yan et al, 2012 ; Lu et al, 2016 ). Samples for qRT-PCR were run in three biological replicates with three technical replicates.…”

De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

“…Complete information on transcriptomes can easily be generated via high-throughput mRNA sequencing technology, which is a powerful and cost-effective tool for gene expression profiling in non-model organisms without a reference genome 10 . Illumina transcriptome de novo sequencing and assembly have been successfully used for Rutaceae plants, with recent research focusing on Citrus 11 – 14 and Pilocarpus species 15 . To the best of our knowledge, no studies have reported transcriptome sequencing of Zanthoxylum .…”

Transcriptome profiles of soybean leaves and roots in response to zinc deficiency

“…Transcriptomic analysis by high-throughput RNA sequencing (RNA-seq) is a useful tool for identifying differentially expressed genes (DEGs) under stress conditions or in tissues of different developmental stages at a genome-wide level (Lu et al 2016, Zeng et al 2016b, Ashoub et al 2018. Recently, transcriptomic analyses were conducted in rice tissues under Zn deficiency for the identification of genes associated with Zn-efficiency and Zn-deficiency responses (Bandyopadhyay et al 2017, Nanda et al 2017.…”