2020 Fiscal Year Research-status Report
Systems biology approach to unravel biosynthesis and evolution of camptothecin, a potent anti-cancer natural product
| Project/Area Number |
19K16391
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| Research Institution | Institute of Physical and Chemical Research |
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Principal Investigator |
Rai Amit 国立研究開発法人理化学研究所, 環境資源科学研究センター, 研究員 (60760535)
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| Project Period (FY) |
2019-04-01 – 2022-03-31
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| Keywords | Metabolic gene clusters / MIAs / Pangenome / Comparative genomics / STR / Evolution / Camptothecin / Secoiridoids |
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| Outline of Annual Research Achievements |
The key findings are as follows. (i) We performed comparative genome analysis using our established chromosome scale genome assembly of Ophiorrhiza pumila to reveal evolutionary basis of monoterpene indole alkaloids biosynthesis. We published our research in Nature communication (Rai et al. Nature Communications volume 12, Article number: 405. 2021). Our study was selected by editors as the most impactful research for 2020-2021 in the field of genomics. (ii) We discovered association of camptothecin biosynthesis with the evolution of strictosidine synthase in the plants, which was the starting point for recruiting biosynthesis enzymes to the camptothecin pathway. (iii) We also reported pangenome of monoterpene indole alkaloids using comparative genomics approach by using four MIA producing plant species including Ophiorrhiza pumila. (iv) We completed whole genome sequencing for Ophiorrhiza japonica, a close relative of Ophiorrhiza pumila with ability to produce several monoterpene indole alkaloids intermediates but not camptothecin. (iv) We also reported putative genes associated with secoiridoids biosynthesis pathways in Cronus officinalis by using our comparative genome analysis approach and resources that we established to study MIA biosynthesis in Ophiorrhiza pumila (DNA Research, Volume 27, Issue 2, April 2020, dsaa009).
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| Current Status of Research Progress |
Current Status of Research Progress
1: Research has progressed more than it was originally planned.
Reason
We have made some significant progress in the last two years to achieve our objective of this project. By the end of these two years, we established high quality chromosome scale genome assembly of camptothecin producing model plant, Ophiorrhiza pumila. We also established complete metabolome resources of Ophiorrhiza pumila. Using comparative genome analysis, we established pangenome of monoterpene indole alkaloids. We also reported newly discovered whole genome duplication event in Camptotheca acuminata genome and identified routes of convergent evolution of camptothecin biosynthesis. We reported evolution of strictosidine biosynthesis as the core and key event that led to the evolution of enzymes involved in the downstream steps of monoterpene indole alkaloids biosynthesis. In a breakthrough, we also acquired whole genome sequencing using high fidelity Pacbio sequencing technology for Ophiorrhiza japonica and Nothapodytes foetida. Nothapodytes foetida genome size was estimated and identified as 9.79Gb. With the requirement of 20x genome coverage to achieve a high-quality genome assembly, we have now achieved 15x genome coverage for N. foetida, and further sequencing will be performed. We will also perform Hi-C library sequencing and sequencing for O. japonica and N. foetida. Whole genome assemblies for these plant species and comparative genome analysis will allow us to identify strong candidate genes involved in the biosynthesis of camptothecin.
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| Strategy for Future Research Activity |
As proposed in our report in the previous year, we could perform whole genome sequencing for O. japonica, and acquired 15x genome coverage sequencing for camptothecin producing plant, N. foetida. In this new year, the main focus will be to achieve followings, (i) To acquire 5x genome coverage of N. foetida as this is essential to derive a high-quality genome assembly. (ii) To perform Hi-C experiment, and library preparation for illumine sequencing for O. japonica and N. foetida. (iii) I will also complete genome assembly for O. japonica and N. foetida. This is one of the main objectives of this year effort. (iv) I will also complete co-expression and integrative omics analysis for Ophiorrhiza pumila hairy roots treated with phytohormones. The transcriptome data was acquired last year, and metabolite profiling is ongoing. The results will be useful to identify candidate genes for future functional characterization. I feel that by the end of this financial year, I will be able to complete whole genome assemblies for O. japonica and N. foetida and would be able to identify genes involved in the camptothecin biosynthesis pathways. I will work towards publication of these results, and my future efforts will be to conduct functional characterization for strong candidate enzymes and to establish sustainable source of camptothecin.
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| Causes of Carryover |
For high fidelity Pacbio sequencing, high molecular weight genomic DNA is required. For N. foetida, the method required longer than expected time for the optimization. I also felt limitation in terms of availability of samples due to coronavirus pandemic. Also, my effort to prepare HiC library for sequencing failed several times before finally being successful in February 2021. Hence, some of the proposed sequencing task were not completed last year. I will perform sequencing for HiC for two plant species as proposed in the research objective. Budget will also be used to meet requirements for data storage, data analysis, and to purchase consumables.
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| Remarks |
The website is Ophiorrhiza pumila genome database, publically available, for use to study MIA biosynthesis in plants.
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[Presentation] Genome-guided multi-omics approach to explore evolution of specialized metabolites in plants2020
Author(s)
Amit Rai, Hideki Hirakawa, Ryo Nakabayashi, Shinji Kikuchi, Koki Hayashi, Megha Rai, Hiroshi Tsugawa Tetsuya Mori, Mami Yamazaki, and Kazuki Saito
Organizer
International plant systems biology, EMBO workshop, April 26-27
Int'l Joint Research / Invited
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