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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.


Venn diagram indicating annotated genes by the KEGG, NR, NT and SwissProt databases.The number of genes annotated is listed in each diagram component.
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pone-0115149-g002: Venn diagram indicating annotated genes by the KEGG, NR, NT and SwissProt databases.The number of genes annotated is listed in each diagram component.

Mentions: The longest transcript in each unigene was selected as the representative transcript. These transcripts were searched against the Nt, Nr, SWISS-PROT and the KEGG databases for annotation. The results indicated that 28,083 (36.2%), 31,392 (40.5%), 22,129 (28.5%) and 19,689 (25.4%) unigenes showed significant similarity to known sequences in the KEGG, Nr, Nt, and SWISS-PROT databases, respectively (Fig. 2). Taken together, 32,943 (42.5%) unigenes were annotated by the four databases.


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)

Venn diagram indicating annotated genes by the KEGG, NR, NT and SwissProt databases.The number of genes annotated is listed in each diagram component.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0115149-g002: Venn diagram indicating annotated genes by the KEGG, NR, NT and SwissProt databases.The number of genes annotated is listed in each diagram component.
Mentions: The longest transcript in each unigene was selected as the representative transcript. These transcripts were searched against the Nt, Nr, SWISS-PROT and the KEGG databases for annotation. The results indicated that 28,083 (36.2%), 31,392 (40.5%), 22,129 (28.5%) and 19,689 (25.4%) unigenes showed significant similarity to known sequences in the KEGG, Nr, Nt, and SWISS-PROT databases, respectively (Fig. 2). Taken together, 32,943 (42.5%) unigenes were annotated by the four databases.

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.