This dataset contains the files associated with the manuscript "A phylogenomic analysis and revised infrageneric classification of Thesium (Santalaceae)" The files listed are the following: 1_README.txt 2_Table_S1_Supplementary material_voucher information.xlsx. Includes taxon name, subgeneric classification, Country of collection, Collector name and Coll. #, Museum depository, Source of plant material, ENA SampleId, ExperimentId and Run AccessionId. Recovery statistics for samples with Angiosperms353 (using the HybPiper script; see https://github.com/mossmatters/HybPiper/wiki#hybpiper-stats) 3_Appendix S2.pdf. Compilation of Hybphaser_Summary_missing_data (HybPhaser script "1b_assess_dataset" ) and Hybphaser_Summary_Paralogs (HybPhaser script "1b_assess_dataset") 3_Hybphaser_Summary_Paralogs.txt is the output from running the HybPhaser script "1b_assess_dataset" which list the loci and loci of particular samples being excluded based the thresholds provided in the config.txt file. 4_SupercontigsThinned.tar.gz : includes all unaligned loci post Treeshrink 5_Cleaned.tar.gz : includes the aligned loci using Mafft for samples with Angiosperms353 (post Treeshrink) 6_IQTree_V2.tar.gz : includes the genes trees generated using IQTree for the each loci matrices for samples with Angiosperms353 7_Astral_V2.tar.gz : is the coalescent astral tree generated with Astral and using ERR7621660 (Buckleya lanceolata) as outgroup.

A phylogenomic analysis and revised infrageneric classification of Thesium (Santalaceae) is presented based on targeted enrichment using the Angiosperms353 probe set. This first targeted sequencing study includes 137 samples representing 106 spe- cies (approximately 32% of the genus). Our results provide substantially improved resolution compared to previous studies that utilised only a few gene regions, with an almost fully supported backbone topology. Thesium (including Austroamericium, Chry- sothesium, Kunkeliella, and Thesidium) is confirmed as monophyletic and sister to a clade containing Lacomucinaea and Osyri- dicarpos. We recognise six monophyletic subgenera with full or strong support: T. subg. Hagnothesium, T. subg. Thesium, T. subg. Spinosa (newly described), T. subg. Discothesium (with revised circumscription), T. subg. Frisea, and T. subg. Psilothesium. We found T. subg. Discothesium as previously delineated to be paraphyletic and describe a new subgenus, T. subg. Spinosa, to ensure monophyly of all subgenera. We formally recognise 18 sections in Thesium, of which 8 are newly described and 2 are raised from lower ranks. Our phylogenetic clades show a strong biogeographic signal and despite sporadic morphological synapomorphies, most subgenera and sections can be distinguished by a combination of their distribution and morphology. We provide the first ge- netic evidence of potential hybridisation in Thesium paving the way for further exploration of this long-hypothesised compounding factor. This study provides a robust framework for future taxonomic, biogeographic, and evolutionary studies of this diverse and problematic genus.