Phylogeny of Orthoptera (Insecta) using targeted ultraconserved element data

Target capture of Ultraconserved Elements (UCEs) is a widely used technique in insect phylogenomic research, with various probe sets developed for different insect orders. However, the use of this approach in the order Orthoptera remains unexplored. In this study, we designed a novel probe set to capture UCE loci in Orthoptera by leveraging annotated Orthoptera genomes. Our designed bait set "Orthoptera-UCEbaitset-v1" contains 15,651 probes of 120 bp each, targeting 1,361 UCE loci. We tested our probe set in-silico by identifying and extracting UCE loci from publicly available genomic and transcriptomic datasets of Orthoptera and additionally, provide alternatives for applying the UCE approach to Orthoptera phylogenomics. The resulting phylogeny from the UCE in-silico test was well-supported and highly similar to the current classification for the group, which is supported by various studies employing diverse sources of evidence. In this study we show that the UCE-based approach provides a compelling alternative to exonic-only genomic targeting, as UCEs span exonic, intronic, and intergenic regions, offering a robust and adaptable solution for Orthoptera phylogenomics. Furthermore, the use of well-established methodologies for probe design and UCE loci capture makes this approach both efficient and scalable, which is particularly valuable for Orthoptera, a group known for its challenging genomic characteristics, including the large genome sizes of many species. Nevertheless, it is crucial to consider that a single strategy may not be universally optimal for phylogenomics of this insect group, and that further studies are needed to evaluate and integrate different approaches for advancing phylogenomic research in Orthoptera.