Characterization of domesticated clove (Syzygium aromaticum) and comparison to related species

PMI-UniNE collaborative PhD project proposal:

Clove (Syzygium aromaticum) is a valuable tree native to Indonesia. Its dried unopened flower buds, and the essential oil extracted either from bud, leaf or stem are commercially used in a wild range of applications within in the pharmaceutical, agricultural, fragrance, flavor and cosmetic industries. Clove is a member of the Myrtaceae family, which includes more than 5650 species split in about 140 genera across all continents. Despite its importance, only few genomics resources are available for species of this family, the best characterized species being Eucalyptus grandis.

In this PhD project, we propose to characterize domesticated clove (S. aromaticum) by developing genomics, metabolomics and genetic resources, and to use these resources to compare clove with relevant species from the Myrtaceae family and with other plant species.

The first step in characterizing S. aromaticum will be to sequence, assemble and annotate a high quality genome. Metabolic pathways from S. aromaticum will also be characterized by obtaining paired transcriptomics and metabolomics data from various tissues and under several conditions. The availability of an annotated genome will enable comparative analysis with genomes of other species in the Myrtaceae family, and the establishment of sequence-based phylogenetic relationships within the family. The conservation of important gene families within related species, including the genes related to the synthesis of the main bioactive compound of the clove, eugenol, will be investigated. Along with other Myrtaceae genomes, the clove genome will then be used to investigate the development of new genotyping markers for this plant family.

The data and results generated from the project are intended to be released into public domain and to be presented at the relevant conferences and published in a peer-reviewed journals.

The sequencing of the clove genome can be performed and analyzed in the Philip Morris Product SA R&D in Neuchatel, while the metabolomics data acquisition and analysis is planned to be performed at the University of Neuchatel.