Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2-3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene-metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.

中文翻译：

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整合转录组和代谢组揭示了参与烟草遗传和环境变异的分子网络。


烟草（Nicotiana tabacum）是种植最广泛的商业非粮食作物之一，具有重大的社会和经济影响。在这里，我们分析了从三个品种（即遗传因素）、三个地点（即环境因素）和六个发育阶段（即发育过程）收集的 54 个烟草样本（2-3 个重复；总共 n = 151）的转录组和代谢组。我们分别鉴定了 3,405 个差异表达 (DE) 基因 (DEG) 和 371 个 DE 代谢物。我们使用定量实时 PCR 验证了 20 个 DEG，并确认了三个位置之间的 18/20 (90%) DEG，以及在各个发育阶段具有相同趋势的 16/20 (80%)。然后，我们构建了九个共表达基因模块和四个共表达代谢物模块，并定义了七个从头调控网络，包括尼古丁和类胡萝卜素相关的调控网络。进一步提出了一种新颖的双向皮尔逊相关方法来整合共表达基因和代谢物模块，以识别联合基因-代谢物关系。最后，我们进一步整合 DE 和网络结果，根据功能重要性对基因进行优先级排序，并确定了排名靠前的新基因 LOC107773232，作为类胡萝卜素代谢途径中涉及的潜在调节因子。因此，这些结果和系统生物学方法为理解烟草复杂的遗传和环境扰动背后的分子机制提供了新的途径。