Author
Listed:
- Amit Rai
(Chiba University
Chiba University
RIKEN Center for Sustainable Resource Science)
- Hideki Hirakawa
(Kazusa DNA Research Institute)
- Ryo Nakabayashi
(RIKEN Center for Sustainable Resource Science)
- Shinji Kikuchi
(Chiba University
Chiba University)
- Koki Hayashi
(Chiba University)
- Megha Rai
(Chiba University)
- Hiroshi Tsugawa
(RIKEN Center for Sustainable Resource Science
RIKEN Center for Integrative Medical Sciences)
- Taiki Nakaya
(Chiba University)
- Tetsuya Mori
(RIKEN Center for Sustainable Resource Science)
- Hideki Nagasaki
(Kazusa DNA Research Institute)
- Runa Fukushi
(Chiba University)
- Yoko Kusuya
(Chiba University)
- Hiroki Takahashi
(Chiba University
Chiba University)
- Hiroshi Uchiyama
(Nihon University)
- Atsushi Toyoda
(National Institute of Genetics)
- Shoko Hikosaka
(Chiba University
Chiba University)
- Eiji Goto
(Chiba University
Chiba University)
- Kazuki Saito
(Chiba University
Chiba University
RIKEN Center for Sustainable Resource Science)
- Mami Yamazaki
(Chiba University
Chiba University)
Abstract
Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.
Suggested Citation
Amit Rai & Hideki Hirakawa & Ryo Nakabayashi & Shinji Kikuchi & Koki Hayashi & Megha Rai & Hiroshi Tsugawa & Taiki Nakaya & Tetsuya Mori & Hideki Nagasaki & Runa Fukushi & Yoko Kusuya & Hiroki Takahas, 2021.
"Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis,"
Nature Communications, Nature, vol. 12(1), pages 1-19, December.
Handle:
RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20508-2
DOI: 10.1038/s41467-020-20508-2
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