Rubiaceae genome evolution

Right: Maximum likelihood plastid tree (RAxML with GTR model of substitution) based on the whole cp sequences of 28 Ixoroideae (with Antirhea chinensis as outgroup) and bootstrap values to estimate the branch support. Left: Circular visualization of annotated Rubiaceae genomes showing the quadripartite structure of Bertiera breviflora. Ly et al., 2020)

The Rubiaceae (coffee family) belong to the Gentianales, in the eudicot family. It is the fourth most species-rich and diverse family of flowering plants, comprising some 13,600 species grouped in around 620 genera and some 60 tribes. Rubiaceae are mainly tropical trees and shrubs, and more rarely annual or perennial grasses. They occupy a wide range of ecological niches, from deserts to evergreen rainforests, and from sea level to high altitudes (over 4,000 m). While some herbaceous species have reached temperate regions, Rubiaceae are particularly abundant (in terms of species diversity and biomass) in lowland rainforests, where they are often the most species-abundant of the woody plant families. The Rubiaceae are divided into two subfamilies, the Rubioideae and the Cinchonoideae, while Bremer and Eriksson recognized three subfamilies, dividing the Cinchonoideae into the Ixoroidae and Cinchonoideae. The pantropical subfamily Ixoroideae comprises around 4,000 species, divided into 27 tribes, and several well-known genera, namely the economically important Coffea and the horticulturally important Gardenia and Ixora, as well as other less economically important genera such as Vangueria, Alibertia and Duroia L.f.

Our aim is to study the phylogenetic relationships between the genera of the subfamily Ixoroideae and to investigate genome evolution using next-generation sequencing data, in collaboration with the Botanical Garden of Meise.

List of publications

Verstraete B, Janssens S, De Block P, Asselman P, Méndez G, Ly S, Hamon P, Guyot R. 2023. Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes. PeerJ 11:e15778.

Ly SN, Garavito A, De Block P, Asselman P, Guyeux C, Charr JC, Janssens S, Mouly A, Hamon P, Guyot R. Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae. PLoS One. 2020 Apr 30;15(4):e0232295. doi: 10.1371/journal.pone.0232295.