This dataset provides phylogenomic resources for studying the evolutionary history of parasitoid wasps in the genus Chelonus (Hymenoptera: Cheloninae), their symbiotic bracoviruses (BVs), and phylogenetic trees generated under multiple analytical frameworks. The data include: 1) Genomic UCE loci: A monolithic FASTA file containing 2,380 untrimmed, unaligned ultraconserved element (UCE) loci from 42 taxa representing all 11 subgenera of Chelonus and related species, generated via the phyluce pipeline. 2) Viral gene alignments: Three datasets comprising aligned sequences of (i) 10 nudivirus genes (NVorf9-1-like, HzNVorf9-2-like, odv-e66-5, 35a-2, 35a-3, 27a, vlf-1a, vlf-1b, vlf-1c, plus one additional core gene), (ii) 2 virulence genes (ANK-CinsV3, CinsV21_orph3), and (iii) combined matrices of both gene categories, identified from 42 chelonine species. Sequences were filtered (alignment length >200 bp, bit score >200) and aligned using MAFFT. 3) Concatenated matrices: Pre-processed phylogenetic matrices (FASTA format) for cophylogenetic analyses, including nudivirus-only, virulence-only, and combined gene sets, concatenated with FASconCAT-G. 4) Phylogenetic trees: Seven species trees reconstructed using six partitioning strategies and two multi-species coalescent (MSC) approaches: 1) Maximum Likelihood (ML): Three partitioning schemes (no partitioning, site-based partitioning, SWSC-EN partitioning). 2) Bayesian Inference (BI): Three partitioning schemes (no partitioning, site-based partitioning, SWSC-EN partitioning). 3) Multi-species coalescent: Trees generated with ASTRAL-III (using 2,116 UCE gene trees) and IQ-TREE v2.0.5. These data support comparative studies on parasitoid-virus coevolution, molecular phylogenetics of Chelonus, and methodological comparisons of partitioning strategies or coalescent vs. concatenation approaches. Researchers can validate host-virus congruence using cophylogenetic analyses (e.g., PACo, tanglegram visualizations), assess topological uncertainty, or integrate UCEs with viral genomic data. The trees provide benchmarks for testing coevolutionary hypotheses or refining analytical pipelines.

UCE loci were obtained using phyluce's get_fastas_from_match_counts script. Viral genes were identified via profile hidden Markov model (HMM) searches using hmmsearch (HMMER v3.3.2) and iterative PSI-BLAST (v2.10.0) with position-specific scoring matrices (PSSMs) against assembled contigs. Reference sequences for 49 virulence and 43 nudivirus genes from the re-annotated CinsBV genome (Mao et al., 2020) were used to construct profile HMMs. Only high-confidence homologs confirmed by both HMMER and PSI-BLAST with alignment coverage ≥50% were retained. Selected genes present in at least 39-40 wasp species were aligned using MAFFT and concatenated with FASconCAT-G. Species trees were inferred using ML (IQ-TREE), BI (MrBayes/BEAST), and MSC methods (ASTRAL-III, IQ-TREE), with gene trees for ASTRAL-III derived from individual UCE loci.