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Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers.

Jiang NH, Zhang GH, Zhang JJ, Shu LP, Zhang W, Long GQ, Liu T, Meng ZG, Chen JW, Yang SC - PLoS ONE (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.

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.

Principal findings: 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.

Conclusion: 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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Dendrogram constructed with UPGMA clustering method among 13 different accessions of E. breviscapus.
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pone-0100357-g009: Dendrogram constructed with UPGMA clustering method among 13 different accessions of E. breviscapus.

Mentions: The polymorphic SSR markers were then used to perform genetic correlation analysis among the 13 E. breviscapus accessions. The UPGMA clustering produced a dendrogram (Figure 9) that separated the 13 E. breviscapus accessions into three groups at the level of genetic similarity 0.93. All local species (YX-1,YX-2,YX-3,and YX-3) formed a cluster. Within the cultivated species, two lines (QS-3 and QS-4) formed a sub-cluster, and the other two lines (QS-1 and QS-2) did not cluster together with other cultivated species. Almost all wild species (MDY-1, MDY-2 and MDY-3) formed a cluster. It is noteworthy that two wild species (MD-1 and MD-2) formed a cluster with the other two cultivated species (QS-3 and QS-4), thus indicated that they may have a similar genetic background. These results demonstrate that SSRs can distinguish varieties without morphological diversities, and they will be a powerful tool for molecular breeding and genetics applications in this herb.


Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers.

Jiang NH, Zhang GH, Zhang JJ, Shu LP, Zhang W, Long GQ, Liu T, Meng ZG, Chen JW, Yang SC - PLoS ONE (2014)

Dendrogram constructed with UPGMA clustering method among 13 different accessions of E. breviscapus.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4067309&req=5

pone-0100357-g009: Dendrogram constructed with UPGMA clustering method among 13 different accessions of E. breviscapus.
Mentions: The polymorphic SSR markers were then used to perform genetic correlation analysis among the 13 E. breviscapus accessions. The UPGMA clustering produced a dendrogram (Figure 9) that separated the 13 E. breviscapus accessions into three groups at the level of genetic similarity 0.93. All local species (YX-1,YX-2,YX-3,and YX-3) formed a cluster. Within the cultivated species, two lines (QS-3 and QS-4) formed a sub-cluster, and the other two lines (QS-1 and QS-2) did not cluster together with other cultivated species. Almost all wild species (MDY-1, MDY-2 and MDY-3) formed a cluster. It is noteworthy that two wild species (MD-1 and MD-2) formed a cluster with the other two cultivated species (QS-3 and QS-4), thus indicated that they may have a similar genetic background. These results demonstrate that SSRs can distinguish varieties without morphological diversities, and they will be a powerful tool for molecular breeding and genetics applications in this herb.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, Yunnan, People's Republic of China.

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.

Principal findings: 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.

Conclusion: 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.

Show MeSH
Related in: MedlinePlus