Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples, Italy.
BMC Genomics. 2019 Jan 15;20(1):43. doi: 10.1186/s12864-019-5428-4.
Tomato is an economically important crop with fruits that are a significant source of bioactive compounds such as ascorbic acid and phenolics. Nowadays, the majority of the enzymes of the biosynthetic pathways and of the structural genes controlling the production and the accumulation of antioxidants in plants are known; however, the mechanisms that regulate the expression of these genes are yet to be investigated. Here, we analyzed the transcriptomic changes occurring during ripening in the fruits of two tomato cultivars (E1 and E115), characterized by a different accumulation of antioxidants, in order to identify candidate genes potentially involved in the biosynthesis of ascorbic acid and phenylpropanoids.
RNA sequencing analyses allowed identifying several structural and regulator genes putatively involved in ascorbate and phenylpropanoids biosynthesis in tomato fruits. Furthermore, transcription factors that may control antioxidants biosynthesis were identified through a weighted gene co-expression network analysis (WGCNA). Results obtained by RNA-seq and WGCNA analyses were further confirmed by RT-qPCR carried out at different ripening stages on ten cultivated tomato genotypes that accumulate different amount of bioactive compounds in the fruit. These analyses allowed us to identify one pectin methylesterase, which may affect the release of pectin-derived D-Galacturonic acid as metabolic precursor of ascorbate biosynthesis. Results reported in the present work allowed also identifying one L-ascorbate oxidase, which may favor the accumulation of reduced ascorbate in tomato fruits. Finally, the pivotal role of the enzymes chalcone synthases (CHS) in controlling the accumulation of phenolic compounds in cultivated tomato genotypes and the transcriptional control of the CHS genes exerted by Myb12 were confirmed.
By using transcriptomic analyses, candidate genes encoding transcription factors and structural genes were identified that may be involved in the accumulation of ascorbic acid and phenylpropanoids in tomato fruits of cultivated genotypes. These analyses provided novel insights into the molecular mechanisms controlling antioxidants accumulation in ripening tomato fruits. The structural genes and regulators here identified could also be used as efficient genetic markers for selecting high antioxidants tomato cultivars.
番茄是一种经济上重要的作物，其果实是生物活性化合物如抗坏血酸和酚类物质的重要来源。如今，植物中生物合成途径的大多数酶和控制抗氧化剂生产和积累的结构基因已经被了解；然而，调节这些基因表达的机制仍有待研究。在这里，我们分析了在两个番茄品种（E1 和 E115）果实成熟过程中发生的转录组变化，这两个品种的抗氧化剂积累不同，目的是鉴定可能参与抗坏血酸和苯丙烷生物合成的候选基因。
RNA 测序分析鉴定了几个结构基因和调节基因，它们可能参与番茄果实中抗坏血酸和苯丙烷的生物合成。此外，通过加权基因共表达网络分析（WGCNA）鉴定了可能控制抗氧化剂生物合成的转录因子。通过在不同成熟阶段对十种积累不同生物活性化合物的栽培番茄基因型进行 RT-qPCR 分析，进一步验证了 RNA-seq 和 WGCNA 分析的结果。这些分析确定了一个果胶甲酯酶，它可能影响果胶衍生的 D-半乳糖醛酸的释放，作为抗坏血酸生物合成的代谢前体。本工作还鉴定了一个 L-抗坏血酸氧化酶，它可能有利于番茄果实中还原型抗坏血酸的积累。最后，证实了查尔酮合酶（CHS）在控制栽培番茄基因型中酚类化合物积累中的关键作用，以及 Myb12 对 CHS 基因转录的控制。
通过转录组分析，鉴定了可能参与栽培番茄品种果实中抗坏血酸和苯丙烷积累的编码转录因子和结构基因的候选基因。这些分析为控制成熟番茄果实中抗氧化剂积累的分子机制提供了新的见解。这里鉴定的结构基因和调节剂也可作为选择高抗氧化剂番茄品种的有效遗传标记。
