A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae
Rubiaceae is among the most species-rich, morphologically, and geographically diverse plant families. Phylogenies have been inferred for many different groups across the family, however these have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae-specific probe set that allows for comparable phylogenetic inference across clades is lacking. Here, we use publicly accessible genomic resources to identify putatively single-copy nuclear loci for target enrichment in two Rubiaceae groups: Hillieae (Cinchonoideae) and Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set and publicly available genomes. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent-aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from different 10 different tribes and three subfamilies, and one outgroup in Apocynaceae. We recovered an average of 75% and 84% of targeted exons and loci respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support at nearly all nodes and evidence of gene tree discordance. Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae.