Full-Length Transcriptome Sequencing and Modular Organization Analysis of the Naringin/Neoeriocitrin-Related Gene Expression Pattern in Drynaria roosii
Full-Length Transcriptome Sequencing and Modular Organization Analysis of the Naringin/Neoeriocitrin-Related Gene Expression Pattern in Drynaria roosii
复制标题
骨碎补柚皮苷/新圣草次苷相关基因表达模式的全长转录组测序和模块化组织分析
DOI：
10.1093/pcp/pcy072
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发表时间：
2018-07
影响因子：
4.9
通讯作者：
Lei Shi
中科院分区：
文献类型：
--
作者：
Meiyu Sun;Jingyi Li;Dong Li;Fengjie Huang;Di Wang;Hui Li;Quan Xing;Huibin Zhu;Lei Shi
槲蕨（Drynaria roosii（Nakaike））是一种传统的中国药用蕨类植物，被称为“骨碎补”。有效成分柚皮苷和新圣草苷具有高度相似的化学结构和药用功能。我们的高效液相色谱-串联质谱（MS/MS）的结果表明，柚苷/新圣草苷的积累依赖于特定的组织或年龄。然而，很少有人知道柚苷/neoeriocitrin相关基因的表达模式参与其调控途径。由于缺乏基本的遗传信息，我们采用单分子实时（SMRT）测序和第二代测序（SGS）相结合的方法来产生完整的全长转录组。罗斯。根据SGS数据，基于差异表达基因（DEG）的热图分析显示，柚苷/新圣枝柑苷相关基因表达具有明显的组织特异性和时间特异性转录组差异。利用系统生物学的模块化组织分析方法，将16,472个DEG聚类为17个基因模块，并研究了模块与组织/时间点样品以及模块与柚苷/新圣草苷含量的关系。我们发现，柚苷/新圣枝柑苷相关的DEG分布在9个不同的模块，在这些模块中的DEG表现出显着不同的模式的转录丰度与特定的组织或年龄。此外，加权基因共表达网络分析（WGCNA）结果进一步证实PAL、4CL和C4 H、C3 H和HCT分别是柚苷和新圣草苷合成的主要枢纽基因，并与MYB和碱性螺旋-亮氨酸-螺旋（bHLH）调控基因表现出高水平的共表达。在这项工作中，模块化组织和共表达网络阐明了基因表达模式的组织和时间特异性，以及与D.罗斯。同时，该转录组数据集为进一步研究D.罗斯。
Drynaria roosii (Nakaike) is a traditional Chinese medicinal fern, known as 'GuSuiBu'. The effective components, naringin and neoeriocitrin, share a highly similar chemical structure and medicinal function. Our HPLC-tandem mass spectrometry (MS/MS) results showed that the accumulation of naringin/neoeriocitrin depended on specific tissues or ages. However, little was known about the expression patterns of naringin/neoeriocitrin-related genes involved in their regulatory pathways. Due to a lack of basic genetic information, we applied a combination of single molecule real-time (SMRT) sequencing and second-generation sequencing (SGS) to generate the complete and full-length transcriptome of D. roosii. According to the SGS data, the differentially expressed gene (DEG)-based heat map analysis revealed that naringin/neoeriocitrin-related gene expression exhibited obvious tissue- and time-specific transcriptomic differences. Using the systems biology method of modular organization analysis, we clustered 16,472 DEGs into 17 gene modules and studied the relationships between modules and tissue/time point samples, as well as modules and naringin/neoeriocitrin contents. We found that naringin/neoeriocitrin-related DEGs distributed in nine distinct modules, and DEGs in these modules showed significantly different patterns of transcript abundance to be linked to specific tissues or ages. Moreover, weighted gene co-expression network analysis (WGCNA) results further identified that PAL, 4CL and C4H, and C3H and HCT acted as the major hub genes involved in naringin and neoeriocitrin synthesis, respectively, and exhibited high co-expression with MYB- and basic helix-leucine-helix (bHLH)-regulated genes. In this work, modular organization and co-expression networks elucidated the tissue and time specificity of the gene expression pattern, as well as hub genes associated with naringin/neoeriocitrin synthesis in D. roosii. Simultaneously, the comprehensive transcriptome data set provided important genetic information for further research on D. roosii.
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