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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 showing the numbers of CYP450 genes expressed across the three tissues.
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pone-0115149-g008: Venn diagram showing the numbers of CYP450 genes expressed across the three tissues.

Mentions: To study the tissue-specific expression of CYP450 genes, we first examined the numbers of genes expressed in the three tissue types. As shown in Fig. 8, a total of 82 CYP450 genes were expressed in all three tissues. Among them, there were 2, 3 and 4 CYP450 genes expressed only in the flower, root and leaf tissues, respectively (Fig. 8). To study the co-expression patterns of CYP450 genes, we performed hierarchical clustering of the expression profiles of these 116 full-length CYP450 genes, SmCPS1, SmKSL1 and SmCYP76AH1 using the Euclidean distance as the metric and Ward’s method. As shown in Fig. 9, six main clusters were readily discernable, which were named C1 to C6. The clusters C1, C4 and C6 possessed the full-length CYP450 genes that showed the highest expression levels in root (37 genes), flower (8 genes) and leaf (31 genes) tissues, respectively. C1 could be further divided into three sub-clusters, C1a, C1b and C1c. C1a had 13 genes, which were expressed similarly in leaf and flower tissues. C1b had 12 genes, which were expressed at the lowest level in the flower tissue. Lastly, C1c had 12 genes, which were expressed at the lowest levels in the leaf tissue. SmCYP76AH1, which is the reference gene involved in tanshinone biosynthesis, together with SmCPS1 and SmKSL1, was found in the cluster C1a and marked with “*” in Fig. 9. Furthermore, the full-length CYP450 genes in clusters C2 (16 genes), C3 (8 genes) and C5 (17 genes) showed the lowest gene expression levels in the flower, leaf and root tissues, respectively. The various expression levels across the different tissue types reflect the unique biological functions of these genes, which need to be elucidated in future studies.


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 showing the numbers of CYP450 genes expressed across the three tissues.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0115149-g008: Venn diagram showing the numbers of CYP450 genes expressed across the three tissues.
Mentions: To study the tissue-specific expression of CYP450 genes, we first examined the numbers of genes expressed in the three tissue types. As shown in Fig. 8, a total of 82 CYP450 genes were expressed in all three tissues. Among them, there were 2, 3 and 4 CYP450 genes expressed only in the flower, root and leaf tissues, respectively (Fig. 8). To study the co-expression patterns of CYP450 genes, we performed hierarchical clustering of the expression profiles of these 116 full-length CYP450 genes, SmCPS1, SmKSL1 and SmCYP76AH1 using the Euclidean distance as the metric and Ward’s method. As shown in Fig. 9, six main clusters were readily discernable, which were named C1 to C6. The clusters C1, C4 and C6 possessed the full-length CYP450 genes that showed the highest expression levels in root (37 genes), flower (8 genes) and leaf (31 genes) tissues, respectively. C1 could be further divided into three sub-clusters, C1a, C1b and C1c. C1a had 13 genes, which were expressed similarly in leaf and flower tissues. C1b had 12 genes, which were expressed at the lowest level in the flower tissue. Lastly, C1c had 12 genes, which were expressed at the lowest levels in the leaf tissue. SmCYP76AH1, which is the reference gene involved in tanshinone biosynthesis, together with SmCPS1 and SmKSL1, was found in the cluster C1a and marked with “*” in Fig. 9. Furthermore, the full-length CYP450 genes in clusters C2 (16 genes), C3 (8 genes) and C5 (17 genes) showed the lowest gene expression levels in the flower, leaf and root tissues, respectively. The various expression levels across the different tissue types reflect the unique biological functions of these genes, which need to be elucidated in future studies.

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.