Lacewing‐specific Universal Single Copy Orthologs designed towards resolution of backbone phylogeny of Neuropterida

Abstract Universal Single Copy Orthologs (USCOs), as a set of markers of nearly universal single‐copy genes, show a superiority in phylogenomic inference. Here, we developed a Benchmarking Universal Single Copy Orthologs (BUSCOs) dataset, neuropterida_odb10, tailored for Neuropterida, based on high‐quality genome assemblies and transcriptome data, comprising 5438 BUSCOs. A range of 1524–5328 complete and single‐copy USCOs could be captured from the genome assemblies and transcriptomes of 104 species of Neuropterida. The reconstruction of a higher‐level phylogeny of Neuropterida based on a comprehensive sampling and refined genomic data in reference to neuropterida_odb10 validates the efficiency of this BUSCO dataset for phylogenomic inference. We recovered Psychopsidae as the sister group to Ithonidae, and corroborated the sister group relationship between Sisyridae and Nevrorthidae within Osmyloidea and the sister group relationship between Chrysopidae and Mantispoidea. Furthermore, our findings highlight that focusing on alignments with a higher presence of parsimony‐informative sites, rather than on the total number of alignments, can diminish errors in gene tree estimation, a process notably vulnerable to error when using multispecies coalescent methods. The neuropterida_odb10 BUSCO reference dataset holds promise for phylogenetic studies at various hierarchical levels, as well as for comparative genomics and the exploration of species diversity within Neuropterida.