Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers.
Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers.
复制标题
三七根转录组分析揭示了假定的三萜皂苷生物合成基因和遗传标记
DOI：
10.1186/1471-2164-12-s5-s5
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发表时间：
2011-12-23
期刊：
影响因子：
4.4
通讯作者：
Chen S
中科院分区：
文献类型：
--
作者：
Luo H;Sun C;Sun Y;Wu Q;Li Y;Song J;Niu Y;Cheng X;Xu H;Li C;Liu J;Steinmetz A;Chen S
背景
三七陈是五加科的重要药用植物。三七中的三萜皂苷类成分是三七中的活性成分。然而，关于这种植物的可用基因组信息是有限的。此外，人参属物种中三萜皂苷生物合成的细节在很大程度上是未知的。
结果
使用454焦磷酸测序技术，四分之一GS FLX钛运行导致三七根的188，185个读数，平均长度为410个碱基。这些读段通过454 GS De Novo Assembler软件处理并组装成30，852个独特序列。通过基本局部比对搜索工具（BLAST）对公共序列数据库的相似性搜索，共有70.2%的独特序列被注释。京都基因和基因组百科全书（KEGG）分配在454-EST数据集中发现了41个独特的序列，代表参与三萜皂苷骨架生物合成的11个基因。特别地，编码达玛烯二醇合酶（DS）的转录物在四年生三七的根中高度表达，达玛烯二醇合酶（DS）是主要三萜皂苷生物合成途径中的第一个关键酶。值得强调的是，通过系统发育分析，分别从174个细胞色素P450和242个糖基转移酶中发现了最可能参与三萜皂苷生物合成的苷元羟基化或糖基化的候选细胞色素P450（Pn 02132和Pn 00158）和UDP-糖基转移酶（Pn 00082）基因。在906个独特序列中检测到推定的转录因子，包括Myb、同源框、WRKY、碱性螺旋-环-螺旋（bHLH）和其他家族蛋白。此外，从2,361个独特序列中鉴定出2,772个简单重复序列（SSR），其中，二核苷酸基序是最丰富的基序。
结论
这项研究是第一个提出了一个大规模的EST数据集三七根获得的下一代测序（NGS）技术。本研究获得了参与三萜皂苷生物合成的候选基因，包括推定的CYP 450和UGT。此外，SSR标记的鉴定为该物种的分子育种和遗传学应用提供了丰富的遗传标记。这些数据将为三七的基因发现、转录调控和分子标记辅助选择提供信息。该数据集为研究奠定了重要基础，旨在确保该物种有足够的药物资源。
Background
Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species are largely unknown.
Results
Using the 454 pyrosequencing technology, a one-quarter GS FLX titanium run resulted in 188,185 reads with an average length of 410 bases for P. notoginseng root. These reads were processed and assembled by 454 GS De Novo Assembler software into 30,852 unique sequences. A total of 70.2% of unique sequences were annotated by Basic Local Alignment Search Tool (BLAST) similarity searches against public sequence databases. The Kyoto Encyclopedia of Genes and Genomes (KEGG) assignment discovered 41 unique sequences representing 11 genes involved in triterpene saponin backbone biosynthesis in the 454-EST dataset. In particular, the transcript encoding dammarenediol synthase (DS), which is the first committed enzyme in the biosynthetic pathway of major triterpene saponins, is highly expressed in the root of four-year-old P. notoginseng. It is worth emphasizing that the candidate cytochrome P450 (Pn02132 and Pn00158) and UDP-glycosyltransferase (Pn00082) gene most likely to be involved in hydroxylation or glycosylation of aglycones for triterpene saponin biosynthesis were discovered from 174 cytochrome P450s and 242 glycosyltransferases by phylogenetic analysis, respectively. Putative transcription factors were detected in 906 unique sequences, including Myb, homeobox, WRKY, basic helix-loop-helix (bHLH), and other family proteins. Additionally, a total of 2,772 simple sequence repeat (SSR) were identified from 2,361 unique sequences, of which, di-nucleotide motifs were the most abundant motif.
Conclusion
This study is the first to present a large-scale EST dataset for P. notoginseng root acquired by next-generation sequencing (NGS) technology. The candidate genes involved in triterpene saponin biosynthesis, including the putative CYP450s and UGTs, were obtained in this study. Additionally, the identification of SSRs provided plenty of genetic makers for molecular breeding and genetics applications in this species. These data will provide information on gene discovery, transcriptional regulation and marker-assisted selection for P. notoginseng. The dataset establishes an important foundation for the study with the purpose of ensuring adequate drug resources for this species.