title: Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Ni-Hao
authors: NH
authors: Jiang
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Guang-Hui
authors: GH
authors: Zhang
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Jia-Jin
authors: JJ
authors: Zhang
authors: Kunming University of Science and Technology, Kunming, Yunnan, People's Republic of China.
authors: Li-Ping
authors: LP
authors: Shu
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Wei
authors: W
authors: Zhang
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Guang-Qiang
authors: GQ
authors: Long
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Tao
authors: T
authors: Liu
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Zheng-Gui
authors: ZG
authors: Meng
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Jun-Wen
authors: JW
authors: Chen
authors: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.
authors: Sheng-Chao
authors: SC
authors: Yang
mesh_terms: D047310:Apigenin / Q000096:biosynthesis*; D002726:Chlorogenic Acid / Q000378:metabolism*; D049919:Erigeron / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D005819:Genetic Markers / Q000235:genetics*; D005965:Glucuronates / Q000096:biosynthesis*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011110:Polymorphism, Genetic / Q000235:genetics; D059467:Transcriptome
chemical_list: D005819:Genetic Markers; D005965:Glucuronates; D010940:Plant Proteins; C484876:scutellarin; D002726:Chlorogenic Acid; D047310:Apigenin