Abstract
In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.
Highlights
Rubiaceae belongs to Gentianales in the eudicots
Among the 28 studied samples 25 exhibited the classical quadripartite structure but three had an apparent tripartite structure with only one IR (Mussaenda pubescens, Feretia aeruginescens and Pavetta schumanniana). These latter belong to three different tribes (Mussaendeae, Octotropideae and Pavetteae, respectively) but the tripartite structure is not present in all representatives of these tribes
Total length ranges from 153,056 bp for Bertiera breviflora to 155,328 bp for Sherbournia buccularia
Summary
Rubiaceae (coffee family) belongs to Gentianales in the eudicots. It is the fourth most speciesrich and diverse family in the flowering plants [1, 2, https://stateoftheworldsplants.org/2017/], comprising ca. Rubiaceae are mainly tropical trees and shrubs, and less often annual or perennial herbs [4]. 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 [5]). 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 [2]. The Rubiaceae are divided into two subfamilies, Rubioideae and Cinchonoideae by [1], whereas Bremer and Eriksson [6] recognized three subfamilies, splitting the Cinchonoideae into Ixoroideae and Cinchonoideae
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