Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly s..., , , # Data from: Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae

[https://doi.org/10.5061/dryad.mpg4f4r67](https://doi.org/10.5061/dryad.mpg4f4r67)

This dataset contains 120 plastome sequences. The sequences were assembled using publically available paired-end Illumina sequencing data.

## Description of the data and file structure

plastomes\_dryad.zip: a zipped folder containing the assembled plastome sequences as .gff annotation files with fasta sequences included.