The Vinca minor genome highlights conserved evolutionary traits in monoterpene indole alkaloid synthesis

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 (MIAs), which are a class of specialized metabolites displaying a wide range of bioactive- and pharmacologically important properties. Within the almost 50 MIAs 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 MIA gene predictions together with a metabolic analysis across four different V. minor tissue types guided the identification of candidate MIA genes. These candidates were finally used to identify MIA 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 MIA gene discovery. It is expected that access to these resources will facilitate the elucidation of unknown MIA biosynthetic routes with the potential of transferring these pathways to heterologous expression systems for large-scale MIA production.

An updated version of the Madagascar periwinkle genome

“…While 38.78% of the genome consisted in TE in C. roseus v.2, a higher proportion (42.87%) was annotated as TE in this new version (v.2.1) with similar distribution across the different TE families ( Figure 2 ). It is worth noting that TE proportion of this v.2.1 is closer to the one in its recently sequenced closely related species Vinca minor ( Stander et al , 2022 ).…”

Genome Assembly of the Medicinal Plant Voacanga thouarsii

“…: Solanaceae. [1] Lamesh et al 2012 ; [2] Hoopes et al 2018 ; [3] Kang et al 2021 ; [4] Franke et al 2019 ; [5] Brose et al 2021 ; [6] Rai et al 2021 ; [7] Guo et al 2018 ; [8] Hosmani et al 2019 ; [9] Stander et al 2022 . …”

“…To infer whole-genome duplication (WGD) events, transcript sequences of V. thouarsii , V. minor ( Stander et al 2022 ), Arabidopsis thaliana ( Lamesh et al 2012 ), Catharanthus roseus ( Franke et al 2019 ), Mytragyna speciosa ( Brose et al 2021 ), Solanum lycopersicum ( Hosmani et al 2019 ), Camptotheca acuminata ( Kang et al 2021 ), Calotropis gigantea ( Hoopes et al 2018 ), G. sempervirens ( Franke et al 2019 ), Ophiorrhiza pumila ( Rai et al 2021 ), and P. somniferum ( Guo et al 2018 ) were input to the DupPipe pipeline ( Barker et al 2010 ). For each dataset, discontiguous MegaBLAST ( Ma et al 2002 , Zhang et al 2004 ) was used to identify duplicated gene pairs (40% sequence similarity over 300 bp).…”

“…Gene families were constructed by comparing the protein sequences of V. thouarsii with ten other plant species: V. minor ( Stander et al 2022 ), A. thaliana ( Lamesh et al 2012 ), Catharanthus roseus ( Franker et al 2019 ), M. speciosa ( Brose et al 2021 ), S. lycopersicum ( Hosmani et al 2019 ), C. acuminata ( Kang et al 2021 ), Calotropis gigantea ( Hoopes et al 2018 ), G. sempervirens ( Franke et al 2019 ), O. pumila ( Rai et al 2021 ) and P. somniferum ( Guo et al 2018 ). Protein sequences of less than 30 amino acids were removed.…”

“…Here, we report the first Voacanga genome assembly. Together with the eight previously published MIA-producing plant genome ( Stander et al 2022 ), this new genome resource will increase our understanding of MIA diversification as well as the evolution of their biosynthetic pathways.…”