Advancing phylogenomic marker design: Updated <scp>USCO</scp> and <scp>UCE</scp> databases of Collembola

Abstract Molecular markers are critical for elucidating the evolution and genetic diversity of species. The relentless progress and innovation in sequencing technology have enabled the acquisition of a vast repository of high‐quality organism genomic data. A more precise and high‐resolution set of molecular markers can provide deeper insights into species evolution. Collembola, as a key group of soil arthropods, has been the focus of extensive research due to its evolutionary and ecological importance. Recently, several chromosome‐level genomes of springtails have been sequenced. Our objective was to enhance molecular marker design to improve the accuracy and robustness of the Collembola database, focusing on universal single‐copy orthologues (USCOs) and ultraconserved elements (UCEs). We constructed a set of 4073 USCOs by examining 15 genomes, including 11 high‐quality genome data at the chromosome level. We then curated and adapted a customized BUSCO (Benchmarking Universal Single‐Copy Orthologues) dataset specifically designed for USCO evaluation. In addition, we developed a novel probe set for UCEs, comprising 67,707 baits targeting 2608 specific loci. We achieved the successful capture of 2089–3847 USCOs and 972–1405 UCEs across the 15 genomes under investigation. These markers were tested to assess their capture success and systematically validated against two previous phylogenomic studies. This approach is instrumental in species identification, phylogenomics, population genetics, and contributes significantly to advancing our understanding of evolutionary biology and ecology. Both datasets are freely available for download from figshare: https://doi.org/10.6084/m9.figshare.26839783 .