Fig. 2

Phylogeny and orthology of Frankliniella occidentalis with other arthropods, with genome and gene set completeness assessments. a The phylogenomic analysis was based on the aligned amino acid sequences of 1604 single-copy orthologs and placed F. occidentalis (shown in red) as basal to the hemipteran species Acyrthosiphon pisum and Cimex lectularius (shown in purple). All nodes have bootstrap support of 100% and the scale bar corresponds to substitutions per site. OrthoDB orthology delineation with the protein-coding genes from the F. occidentalis official gene set identify genes with orthologs in all or most of the representative insects and the outgroup species, Daphnia pulex, as well as those with more limited distributions or with no confidently identifiable arthropod orthologs. b Assessments using the 1066 arthropod Benchmarking Universal Single-Copy Orthologs (BUSCOs) show few missing genes (5 for the assembly, 4 for the OGS) from F. occidentalis, with better OGS completeness than A. pisum, C. lectularius, and P. humanus. The F. occidentalis official gene set (OGS) scores better than its genome assembly, indicating that the gene annotation strategy has successfully managed to capture even difficult to annotate genes. The left bars for each species, also outlined with a dashed line, show the results based on the genome, whereas the right bars show the results for the OGSs. Species names abbreviations: Dmela—Drosophila melanogaster, Dplex—Danaus plexippus, Tcast—Tribolium castaneum, Amell—Apis mellifera, Phuma—Pediculus humanus, Apisu—Acyrthosiphon pisum, Clect—Cimex lectularius, Focci—Frankliniella occidentalis, Dpule—Daphnia pulex