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RNA-seq Transcriptome Analysis of Panax japonicus and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis

机译：人参的RNA-seq转录组分析及其与其他人参物种的比较以鉴定涉及皂苷生物合成的潜在基因

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The Panax genus has been a source of natural medicine, benefitting human health over the ages, among which the Panax japonicus represents an important species. Our understanding of several key pathways and enzymes involved in the biosynthesis of ginsenosides, a pharmacologically active class of metabolites and a major chemical constituents of the rhizome extracts from the Panax species, are limited. Limited genomic information, and lack of studies on comparative transcriptomics across the Panax species have restricted our understanding of the biosynthetic mechanisms of these and many other important classes of phytochemicals. Herein, we describe Illumina based RNA sequencing analysis to characterize the transcriptome and expression profiles of genes expressed in the five tissues of P. japonicus, and its comparison with other Panax species. RNA sequencing and de novo transcriptome assembly for P. japonicus resulted in a total of 135,235 unigenes with 78,794 (58.24%) unigenes being annotated using NCBI-nr database. Transcriptome profiling, and gene ontology enrichment analysis for five tissues of P. japonicus showed that although overall processes were evenly conserved across all tissues. However, each tissue was characterized by several unique unigenes with the leaves showing the most unique unigenes among the tissues studied. A comparative analysis of the P. japonicus transcriptome assembly with publically available transcripts from other Panax species, namely, P. ginseng, P. notoginseng, and P. quinquefolius also displayed high sequence similarity across all Panax species, with P. japonicus showing highest similarity with P. ginseng. Annotation of P. japonicus transcriptome resulted in the identification of putative genes encoding all enzymes from the triterpene backbone biosynthetic pathways, and identified 24 and 48 unigenes annotated as cytochrome P450 (CYP) and glycosyltransferases (GT), respectively. These CYPs and GTs annotated unigenes were conserved across all Panax species and co-expressed with other the transcripts involved in the triterpenoid backbone biosynthesis pathways. Unigenes identified in this study represent strong candidates for being involved in the triterpenoid saponins biosynthesis, and can serve as a basis for future validation studies.
机译：人参属一直是天然药物的来源，多年来有益于人类健康，其中人参是重要的物种。我们对人参皂苷生物合成，药理学活性的代谢产物和人参根茎提取物的主要化学成分的几种关键途径和酶的了解是有限的。有限的基因组信息，以及缺乏对全人类物种比较转录组学的研究，限制了我们对这些以及许多其他重要植物化学物质的生物合成机制的理解。在这里，我们描述了基于Illumina的RNA测序分析，以表征在日本对虾的五个组织中表达的基因的转录组和表达谱，并将其与其他人参物种进行比较。日本对虾的RNA测序和从头转录组组装产生了总共135,235个单基因，其中使用NCBI-nr数据库注释了78,794个（58.24％）单基因。对日本对虾的五个组织进行转录组分析和基因本体分析表明，尽管整个过程在所有组织中均被保守。但是，每个组织的特征是几个独特的单基因，叶子显示了所研究组织中最独特的单基因。对日本对虾转录组装配体与其他人参物种人参，三七和西洋参的转录本的比较分析也显示了所有人种之间的高度序列相似性，日本对虾显示出最高的相似性与人参。 P的注释。 japonicus 转录组从三萜骨架生物合成途径中鉴定出编码所有酶的推定基因，并分别鉴定了分别标记为细胞色素P450（CYP）和糖基转移酶（GT）的24和48个单基因。这些CYP和GTs注释的单基因在所有 Panax 物种中均保守，并与参与三萜骨架生物合成途径的其他转录本共表达。在这项研究中鉴定出的Unigenes是参与三萜皂苷生物合成的有力候选者，可作为未来验证研究的基础。

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