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Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in Salvia miltiorrhiza.

Chen H, Wu B, Nelson DR, Wu K, Liu C - PLoS ONE (2014)

Bottom Line: The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff.Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis.Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9).

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

ABSTRACT
Salvia miltiorrhiza is one of the most economically important medicinal plants. Cytochrome P450 (CYP450) genes have been implicated in the biosynthesis of its active components. However, only a dozen full-length CYP450 genes have been described, and there is no systematic classification of CYP450 genes in S. miltiorrhiza. We obtained 77,549 unigenes from three tissue types of S. miltiorrhiza using RNA-Seq technology. Combining our data with previously identified CYP450 sequences and scanning with the CYP450 model from Pfam resulted in the identification of 116 full-length and 135 partial-length CYP450 genes. The 116 genes were classified into 9 clans and 38 families using standard criteria. The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff. The expression profiles for 16 of 19 randomly selected CYP450 obtained from RNA-Seq were validated by qRT-PCR. Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis. Considering all the evidence, 3 CYP450 genes were identified to be potentially involved in terpenoid biosynthesis. Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9). Lastly, a web resource (SMCYP450, http://www.herbalgenomics.org/samicyp450) was set up, which allows users to browse, search, retrieve and compare CYP450 genes and can serve as a centralized resource.

No MeSH data available.


Sequence length distribution of the assembled transcripts.The X-axis shows the range of lengths of the transcript sequences. The Y-axis shows the percentage of transcripts.
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pone-0115149-g001: Sequence length distribution of the assembled transcripts.The X-axis shows the range of lengths of the transcript sequences. The Y-axis shows the percentage of transcripts.

Mentions: A total of 25.3, 53.8 and 26.7 million 100-bp paired end reads were generated from the flower, leaf and root samples, respectively. Then, the unigenes were assembled from the pooled reads of the three tissues using Trinity [30]. The resulting assembly contained 77,549 unigenes. As some unigenes contained multiple alternatively spliced transcripts, there were a total of 137,856 unique transcripts. The length of these transcripts ranged from 201 to 12,362 bp, with an average length of 933 bp (Fig. 1). The RNA-Seq data can be accessed from NCBI with the accession numbers SRR1043988, SRR1045051 and SRR1020591.


Computational Identification and Systematic Classification of Novel Cytochrome P450 Genes in Salvia miltiorrhiza.

Chen H, Wu B, Nelson DR, Wu K, Liu C - PLoS ONE (2014)

Sequence length distribution of the assembled transcripts.The X-axis shows the range of lengths of the transcript sequences. The Y-axis shows the percentage of transcripts.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4262458&req=5

pone-0115149-g001: Sequence length distribution of the assembled transcripts.The X-axis shows the range of lengths of the transcript sequences. The Y-axis shows the percentage of transcripts.
Mentions: A total of 25.3, 53.8 and 26.7 million 100-bp paired end reads were generated from the flower, leaf and root samples, respectively. Then, the unigenes were assembled from the pooled reads of the three tissues using Trinity [30]. The resulting assembly contained 77,549 unigenes. As some unigenes contained multiple alternatively spliced transcripts, there were a total of 137,856 unique transcripts. The length of these transcripts ranged from 201 to 12,362 bp, with an average length of 933 bp (Fig. 1). The RNA-Seq data can be accessed from NCBI with the accession numbers SRR1043988, SRR1045051 and SRR1020591.

Bottom Line: The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff.Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis.Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9).

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

ABSTRACT
Salvia miltiorrhiza is one of the most economically important medicinal plants. Cytochrome P450 (CYP450) genes have been implicated in the biosynthesis of its active components. However, only a dozen full-length CYP450 genes have been described, and there is no systematic classification of CYP450 genes in S. miltiorrhiza. We obtained 77,549 unigenes from three tissue types of S. miltiorrhiza using RNA-Seq technology. Combining our data with previously identified CYP450 sequences and scanning with the CYP450 model from Pfam resulted in the identification of 116 full-length and 135 partial-length CYP450 genes. The 116 genes were classified into 9 clans and 38 families using standard criteria. The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff. The expression profiles for 16 of 19 randomly selected CYP450 obtained from RNA-Seq were validated by qRT-PCR. Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis. Considering all the evidence, 3 CYP450 genes were identified to be potentially involved in terpenoid biosynthesis. Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9). Lastly, a web resource (SMCYP450, http://www.herbalgenomics.org/samicyp450) was set up, which allows users to browse, search, retrieve and compare CYP450 genes and can serve as a centralized resource.

No MeSH data available.