Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers.
Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers.
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对灯盏花转录组的分析揭示了假定的灯盏乙素和绿原酸生物合成基因和遗传标记。
DOI：
10.1371/journal.pone.0100357
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Yang SC
中科院分区：
文献类型：
--
作者：
Jiang NH;Zhang GH;Zhang JJ;Shu LP;Zhang W;Long GQ;Liu T;Meng ZG;Chen JW;Yang SC
灯盏花 (Vant.) Hand-Mazz。是一种著名的药用植物。灯盏乙素和绿原酸是这种草药的主要活性成分。然而，灯盏花乙素和绿原酸在短茎中的生物合成和调节机制尚不清楚。此外，这种草药的基因组信息也无法获得。使用 GAIIx 平台上的 Illumina 测序，总共生成了 64,605,972 个原始测序读数，并组装成 73,092 个非冗余 unigene。其中，44,855个unigenes（61.37%）在公共数据库Nr、Swiss-Prot、KEGG和COG中被注释。在 Illumina 数据集中发现了编码参与类黄酮和绿原酸生物合成的已知酶的转录本。发现了三个候选细胞色素 P450 基因，它们可能编码将芹菜素转化为灯盏花素的黄酮 6-水解酶。此外，还定义了编码玉米P1同源物（R2R3-MYB转录因子）的4个unigenes，它们可能调节灯盏乙素的生物合成。此外，从 9,255 个 unigene 中总共鉴定出 11,077 个简单序列重复 (SSR)。在 SSR 中，三核苷酸基序是最丰富的基序。随机选择 36 对 SSR 引物对扩增和多态性进行验证。结果显示，34对（94.40%）引物被成功扩增，19对（52.78%）引物出现多态性。本研究利用二代测序（NGS）技术，首次提供了短柄桉的丰富基因组数据。本研究获得了参与灯盏花乙素和绿原酸生物合成及转录调控的候选基因。此外，通过SSR的鉴定产生了大量的遗传标记，这是该草药分子育种和遗传学应用的有力工具。
Erigeron breviscapus (Vant.) Hand-Mazz. is a famous medicinal plant. Scutellarin and chlorogenic acids are the primary active components in this herb. However, the mechanisms of biosynthesis and regulation for scutellarin and chlorogenic acids in E. breviscapus are considerably unknown. In addition, genomic information of this herb is also unavailable. Using Illumina sequencing on GAIIx platform, a total of 64,605,972 raw sequencing reads were generated and assembled into 73,092 non-redundant unigenes. Among them, 44,855 unigenes (61.37%) were annotated in the public databases Nr, Swiss-Prot, KEGG, and COG. The transcripts encoding the known enzymes involved in flavonoids and in chlorogenic acids biosynthesis were discovered in the Illumina dataset. Three candidate cytochrome P450 genes were discovered which might encode flavone 6-hydroase converting apigenin to scutellarein. Furthermore, 4 unigenes encoding the homologues of maize P1 (R2R3-MYB transcription factors) were defined, which might regulate the biosynthesis of scutellarin. Additionally, a total of 11,077 simple sequence repeat (SSR) were identified from 9,255 unigenes. Of SSRs, tri-nucleotide motifs were the most abundant motif. Thirty-six primer pairs for SSRs were randomly selected for validation of the amplification and polymorphism. The result revealed that 34 (94.40%) primer pairs were successfully amplified and 19 (52.78%) primer pairs exhibited polymorphisms. Using next generation sequencing (NGS) technology, this study firstly provides abundant genomic data for E. breviscapus. The candidate genes involved in the biosynthesis and transcriptional regulation of scutellarin and chlorogenic acids were obtained in this study. Additionally, a plenty of genetic makers were generated by identification of SSRs, which is a powerful tool for molecular breeding and genetics applications in this herb.
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