Transcriptome analysis of methyl jasmonate-elicited Panax ginseng adventitious roots to discover putative ginsenoside biosynthesis and transport genes.
Transcriptome analysis of methyl jasmonate-elicited Panax ginseng adventitious roots to discover putative ginsenoside biosynthesis and transport genes.
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DOI：
10.3390/ijms16023035
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发表时间：
2015-01-29
影响因子：
5.6
通讯作者：
Luo Z
中科院分区：
文献类型：
--
作者：
Cao H;Nuruzzaman M;Xiu H;Huang J;Wu K;Chen X;Li J;Wang L;Jeong JH;Park SJ;Yang F;Luo J;Luo Z
人参（Panax ginseng C.A.）Meyer属于五加科，长期以来一直被用作草药。虽然公共数据库目前可用于这个家庭，没有茉莉酸甲酯（MeJA）引起的转录组信息是以前报道的这个物种，除了一些表达序列标签（EST）使用传统的桑格方法。在此，通过Illumina HiSeq™2000从用MeJA（Pg-MeJA）和等体积的溶剂乙醇（Pg-Con）处理的两个样品中分别过滤约5300万个不定根转录组的干净读数。共同地，来自两个样品的总共71，095个全unigenes被组装和注释，并且基于与已知蛋白质的序列相似性搜索，总共获得56，668个unigenes。在这些注释的单基因中，54，920个被分配到NCBI非冗余蛋白（Nr）数据库，35，448个分配到Swiss-prot数据库，43，051个分配到基因本体（GO），19，986个分配到直链组簇（COG）。在京都基因和基因组百科全书（KEGG）通路数据库中搜索表明，32，200个单基因被定位到128个KEGG通路。此外，我们获得了几个基因显示了广泛的表达水平。我们还确定了总共749个β-内酰胺生物合成酶基因和12个有前途的多效性耐药（PDR）基因与β-内酰胺转运。
The Panax ginseng C.A. Meyer belonging to the Araliaceae has long been used as an herbal medicine. Although public databases are presently available for this family, no methyl jasmonate (MeJA) elicited transcriptomic information was previously reported on this species, with the exception of a few expressed sequence tags (ESTs) using the traditional Sanger method. Here, approximately 53 million clean reads of adventitious root transcriptome were separately filtered via Illumina HiSeq™2000 from two samples treated with MeJA (Pg-MeJA) and equal volumes of solvent, ethanol (Pg-Con). Jointly, a total of 71,095 all-unigenes from both samples were assembled and annotated, and based on sequence similarity search with known proteins, a total of 56,668 unigenes was obtained. Out of these annotated unigenes, 54,920 were assigned to the NCBI non-redundant protein (Nr) database, 35,448 to the Swiss-prot database, 43,051 to gene ontology (GO), and 19,986 to clusters of orthologous groups (COG). Searching in the Kyoto encyclopedia of genes and genomes (KEGG) pathway database indicated that 32,200 unigenes were mapped to 128 KEGG pathways. Moreover, we obtained several genes showing a wide range of expression levels. We also identified a total of 749 ginsenoside biosynthetic enzyme genes and 12 promising pleiotropic drug resistance (PDR) genes related to ginsenoside transport.
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