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Stander EA, Cuello C, Birer-Williams C, Kulagina N, Jansen HJ, Carqueijeiro I, Méteignier LV, Vergès V, Oudin A, Papon N, Dirks RP, Jensen MK, O’Connor SE, Dugé de Bernonville T, Besseau S, Courdavault V. The Vinca minor genome highlights conserved evolutionary traits in monoterpene indole alkaloid synthesis. G3 (Bethesda) 2022; 12:jkac268. [PMID: 36200869 PMCID: PMC9713385 DOI: 10.1093/g3journal/jkac268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2023]
Abstract
Vinca minor, also known as the lesser periwinkle, is a well-known species from the Apocynaceae, native to central and southern Europe. This plant synthesizes monoterpene indole alkaloids, which are a class of specialized metabolites displaying a wide range of bioactive- and pharmacologically important properties. Within the almost 50 monoterpene indole alkaloids it produces, V. minor mainly accumulates vincamine, which is commercially used as a nootropic. Using a combination of Oxford Nanopore Technologies long read- and Illumina short-read sequencing, a 679,098 Mb V. minor genome was assembled into 296 scaffolds with an N50 scaffold length of 6 Mb, and encoding 29,624 genes. These genes were functionally annotated and used in a comparative genomic analysis to establish gene families and to investigate gene family expansion and contraction across the phylogenetic tree. Furthermore, homology-based monoterpene indole alkaloid gene predictions together with a metabolic analysis across 4 different V. minor tissue types guided the identification of candidate monoterpene indole alkaloid genes. These candidates were finally used to identify monoterpene indole alkaloid gene clusters, which combined with synteny analysis allowed for the discovery of a functionally validated vincadifformine-16-hydroxylase, reinforcing the potential of this dataset for monoterpene indole alkaloids gene discovery. It is expected that access to these resources will facilitate the elucidation of unknown monoterpene indole alkaloid biosynthetic routes with the potential of transferring these pathways to heterologous expression systems for large-scale monoterpene indole alkaloid production.
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Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Natalja Kulagina
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Ines Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Sarah Ellen O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
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