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)
Rubiaceae (coffee family) belongs to Gentianales in the eudicots. It is the fourth most species-rich and diverse family in the flowering plants, comprising ca. 13,600 species grouped in ca. 620 genera and ca. 60 tribes. Rubiaceae are mainly tropical trees and shrubs, and less often annual or perennial herbs. They occupy a large range of ecological niches from desert to evergreen humid forests and from sea level to high altitudes (above 4,000 m ). While some herbaceous species reached the temperate regions, Rubiaceae are especially abundant (species diversity and biomass) in lowland humid tropical forest, where they often are the most species-abundant of the woody plant families. The Rubiaceae are divided into two subfamilies, Rubioideae and Cinchonoideae, whereas Bremer and Eriksson recognized three subfamilies, splitting the Cinchonoideae into Ixoroideae and Cinchonoideae. The pantropical Ixoroideae subfamily comprises ca. 4,000 species, distributed into 27 tribes, and several well-known genera, i.e. the economically important Coffea and the horticulturally important Gardenia and Ixora, besides other less economically important genera such as Vangueria, Alibertia and Duroia L.f.
Our objective is to study the phylogenetic relationships between the genera of the subfamily Ixoroideae and to study the evolution of the genome using next generation sequencing data, in collaboration with the Meise Botanical Garden.
List of publications
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.