Identification of pivotal genes associated with sugar and organic acid metabolism during Prunus Mume fruit ripening via metabolomic and transcriptomic analyses

The fruit of Prunus mume, a plant with medicinal and edible properties, contains sugars and organic acids as its vital ingredients, yet, their metabolic characteristics and regulatory mechanisms remain unclear. This study firstly investigated the metabolic dynamics of sugars and organic acids during four stages of fruit ripening, and hence sucrose and citrate were identified as the predominant sugar and organic acid, respectively. ABA correlated positively with citrate and sucrose accumulation. Then, 79.60 Gb transcriptome sequencing of four different stages facilitated the identification of candidate genes playing role in accumulation of sugars and organic acids, respectively. As a result, sucrose accumulation was associated with upregulation of SPS (LOC103341128), SUS (LOC103323057) and glgc (LOC103320871), alongside the downregulation of INVs (LOC103337231, LOC103333352, and LOC103341755). Citrate accumulation was largely driven by the upregulation of PEPC (LOC103318857) and CS (LOC103328745), and downregulation of NADP-IDH (LOC103340345) and GS (LOC103321068, LOC103338669). Enzymatic assay confirmed that CS (LOC103328745) encoded a functional enzyme in TCA cycle. Furthermore, correlation along with clustering analyses reinforced the close linkage among ABA, citrate and sucrose during fruit ripening. Beyond the metabolic enzymes, 328 transcription factors and 97 ABC transporters showing positive correlation with a least one type of sugar or organic acid might be responsible for the regulation and transportation of sugars and organic acids metabolism. Among them, AP2 (LOC103337713) was proposed as the core transcription factor by protein-protein interactome analysis and ABA was highlighted as a central regulatory switch governing sugar and organic acid metabolism in P. mume. This work provides not only valuable insights into the regulative mechanism of fruit sweetness and acidity in P. mume, but also potential strategy for further agricultural application in quality improvement of P. mume.