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 family, a cornerstone of the Gentianales order within the eudicots, ranks as the fourth largest and most diverse family of flowering plants. It boasts approximately 13,600 species spread across about 620 genera and 60 tribes. Characterized predominantly as tropical trees and shrubs, with a minority manifesting as annual or perennial grasses, Rubiaceae span a vast array of ecological habitats. Their adaptability ranges from arid deserts to lush evergreen rainforests, and from sea-level terrains to elevations exceeding 4,000 meters. Although a selection of herbaceous species has ventured into temperate zones, the Rubiaceae's greatest species diversity and biomass concentration are found within lowland rainforests, where they frequently dominate as the most species-rich woody plant family.

Taxonomically, the Rubiaceae are segmented into two principal subfamilies: the Rubioideae and the Cinchonoideae. An alternative classification by Bremer and Eriksson introduces a tripartite division, further splitting the Cinchonoideae into the Ixoroidae and Cinchonoideae subfamilies. The Ixoroideae, a pantropical subfamily, encompasses roughly 4,000 species across 27 tribes, incorporating several notable genera. Among these, Coffea stands out for its economic significance, while Gardenia and Ixora are prized for their horticultural value. Additionally, other genera like Vangueria, Alibertia, and Duroia L.f., though less commercially pivotal, contribute to the subfamily's richness.

Our research endeavors to unravel the phylogenetic intricacies among the Ixoroideae genera, employing advanced next-generation sequencing technologies. In partnership with the Botanical Garden of Meise, we aim to shed light on the genome evolution within this subfamily, paving the way for a deeper understanding of its biological and ecological diversity. This collaborative effort seeks not only to enhance our comprehension of the Ixoroideae's complex genetic heritage but also to contribute to the broader field of plant evolutionary biology.

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.