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 tribes: Hillieae (Cinchonoideae) and Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exons corresponding to 1059 supercontigs in our target clades, and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. Our probe set, which we call Rubiaceae 2270, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.