De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids
Aconitum carmichaelii is an important medicinal herb used widely in China, Japan, India, Korea, and other Asian countries. While extensive research on the characterization of metabolic extracts of A. carmichaelii has shown accumulation of numerous bioactive metabolites including aconitine and aconit...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2017-12-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/22/12/2155 |
| _version_ | 1811303852814630912 |
|---|---|
| author | Megha Rai Amit Rai Noriaki Kawano Kayo Yoshimatsu Hiroki Takahashi Hideyuki Suzuki Nobuo Kawahara Kazuki Saito Mami Yamazaki |
| author_facet | Megha Rai Amit Rai Noriaki Kawano Kayo Yoshimatsu Hiroki Takahashi Hideyuki Suzuki Nobuo Kawahara Kazuki Saito Mami Yamazaki |
| author_sort | Megha Rai |
| collection | DOAJ |
| description | Aconitum carmichaelii is an important medicinal herb used widely in China, Japan, India, Korea, and other Asian countries. While extensive research on the characterization of metabolic extracts of A. carmichaelii has shown accumulation of numerous bioactive metabolites including aconitine and aconitine-type diterpene alkaloids, its biosynthetic pathway remains largely unknown. Biosynthesis of these secondary metabolites is tightly controlled and mostly occurs in a tissue-specific manner; therefore, transcriptome analysis across multiple tissues is an attractive method to identify the molecular components involved for further functional characterization. In order to understand the biosynthesis of secondary metabolites, Illumina-based deep transcriptome profiling and analysis was performed for four tissues (flower, bud, leaf, and root) of A. carmichaelii, resulting in 5.5 Gbps clean RNA-seq reads assembled into 128,183 unigenes. Unigenes annotated as possible rate-determining steps of an aconitine-type biosynthetic pathway were highly expressed in the root, in accordance with previous reports describing the root as the accumulation site for these metabolites. We also identified 21 unigenes annotated as cytochrome P450s and highly expressed in roots, which represent candidate unigenes involved in the diversification of secondary metabolites. Comparative transcriptome analysis of A. carmichaelii with A. heterophyllum identified 20,232 orthogroups, representing 30,633 unigenes of A. carmichaelii, gene ontology enrichment analysis of which revealed essential biological process together with a secondary metabolic process to be highly enriched. Unigenes identified in this study are strong candidates for aconitine-type diterpene alkaloid biosynthesis, and will serve as useful resources for further validation studies. |
| first_indexed | 2024-04-13T07:55:32Z |
| format | Article |
| id | doaj.art-2acc7fb0cf624dcdae83b39a325de719 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-04-13T07:55:32Z |
| publishDate | 2017-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-2acc7fb0cf624dcdae83b39a325de7192022-12-22T02:55:25ZengMDPI AGMolecules1420-30492017-12-012212215510.3390/molecules22122155molecules22122155De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene AlkaloidsMegha Rai0Amit Rai1Noriaki Kawano2Kayo Yoshimatsu3Hiroki Takahashi4Hideyuki Suzuki5Nobuo Kawahara6Kazuki Saito7Mami Yamazaki8Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanGraduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanTsukuba Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba 305-0843, JapanTsukuba Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba 305-0843, JapanMedical Mycology Research Center, Chiba University, Chiba 260-8673, JapanKazusa DNA Research Institute, Chiba 292-0818, JapanTsukuba Division, Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba 305-0843, JapanGraduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanGraduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, JapanAconitum carmichaelii is an important medicinal herb used widely in China, Japan, India, Korea, and other Asian countries. While extensive research on the characterization of metabolic extracts of A. carmichaelii has shown accumulation of numerous bioactive metabolites including aconitine and aconitine-type diterpene alkaloids, its biosynthetic pathway remains largely unknown. Biosynthesis of these secondary metabolites is tightly controlled and mostly occurs in a tissue-specific manner; therefore, transcriptome analysis across multiple tissues is an attractive method to identify the molecular components involved for further functional characterization. In order to understand the biosynthesis of secondary metabolites, Illumina-based deep transcriptome profiling and analysis was performed for four tissues (flower, bud, leaf, and root) of A. carmichaelii, resulting in 5.5 Gbps clean RNA-seq reads assembled into 128,183 unigenes. Unigenes annotated as possible rate-determining steps of an aconitine-type biosynthetic pathway were highly expressed in the root, in accordance with previous reports describing the root as the accumulation site for these metabolites. We also identified 21 unigenes annotated as cytochrome P450s and highly expressed in roots, which represent candidate unigenes involved in the diversification of secondary metabolites. Comparative transcriptome analysis of A. carmichaelii with A. heterophyllum identified 20,232 orthogroups, representing 30,633 unigenes of A. carmichaelii, gene ontology enrichment analysis of which revealed essential biological process together with a secondary metabolic process to be highly enriched. Unigenes identified in this study are strong candidates for aconitine-type diterpene alkaloid biosynthesis, and will serve as useful resources for further validation studies.https://www.mdpi.com/1420-3049/22/12/2155AconitumRNA sequencingtranscript abundancediterpene alkaloidsaconitineKEGG pathway enrichment analysis |
| spellingShingle | Megha Rai Amit Rai Noriaki Kawano Kayo Yoshimatsu Hiroki Takahashi Hideyuki Suzuki Nobuo Kawahara Kazuki Saito Mami Yamazaki De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids Molecules Aconitum RNA sequencing transcript abundance diterpene alkaloids aconitine KEGG pathway enrichment analysis |
| title | De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids |
| title_full | De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids |
| title_fullStr | De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids |
| title_full_unstemmed | De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids |
| title_short | De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids |
| title_sort | de novo rna sequencing and expression analysis of aconitum carmichaelii to analyze key genes involved in the biosynthesis of diterpene alkaloids |
| topic | Aconitum RNA sequencing transcript abundance diterpene alkaloids aconitine KEGG pathway enrichment analysis |
| url | https://www.mdpi.com/1420-3049/22/12/2155 |
| work_keys_str_mv | AT megharai denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids AT amitrai denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids AT noriakikawano denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids AT kayoyoshimatsu denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids AT hirokitakahashi denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids AT hideyukisuzuki denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids AT nobuokawahara denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids AT kazukisaito denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids AT mamiyamazaki denovornasequencingandexpressionanalysisofaconitumcarmichaeliitoanalyzekeygenesinvolvedinthebiosynthesisofditerpenealkaloids |