The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Nathalie Raharimalala,Andréa Garavito,Solène Froger,Stéphane Michaux,J J R Rakotomalala ,Romain Guyot,Laurence Bellanger,Emmanuel Couturon,Victoria Berry,Alexa Yadira Morales-Correa,A.a Mccarthy ,Simón Orozco-Arias ,Perla Hamon,Coralie Fournier,Patrick Descombes,Lukas A Mueller ,Maud Lepelley,Stéphane Rombauts ,Sylviane Métairon ,Dominique Crouzillat

doi:10.1038/s41598-021-87419-0

Abstract

Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

Highlights

Caffeine is the most consumed alkaloid stimulant in the world
We postulate here that it is the loss of the Caffeine Synthase (DXMT) gene through an illegitimate recombination mechanism, which is likely involved in the absence of caffeine
The 11 largest scaffolds correspond to 88.7% (374.5 Mb) of the total size of the assembly and 92.5% of the k-merbased genome size with pseudo-chromosome sizes ranging from 26,432,012 to 57,522,413 bp

Summary

Introduction

Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. We are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. The absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturallydecaffeinated coffee drinks for consumers. Our analyses encompass unprecedented information characterizing the genome of a wild caffeine-free species in the Coffea genus and bring forth a significant contribution towards developing a naturally-decaffeinated coffee drink

Methods

Results

Conclusion