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sai 1989). Dataset and partition scheme including chosen models are offered in the Dryad digital repository. Phylogenetic relationships were inferred beneath the maximum likelihood (ML) optimality criterion as implemented in IQ-TREE v. 1.six.12 (Chernomor et al. 2016; Nguyen et al. 2015) using the most beneficial scoring aa substitution matrix for every single gene partition plus the edge-proportional partition model allowing partitions to possess distinct evolutionary rates (option -ssp). We performed 50 independent tree searches (25 searches using a CA Ⅱ Inhibitor Compound random and 25 with a parsimony start tree). The resulting variety of unique tree topologies was assessed with Special Tree v. 1.9, kindly provided by Thomas Wong and available upon request. Node help was estimated by means of nonparametric bootstrapping of 100 bootstraps replicates in IQ-TREE and mapped onto the ML tree using the finest loglikelihood. We further scanned all these lepidopteran protein sets for many gene families connected with detoxification function, namely P450 monooxygenases (P450s), carboxyl- and choline esterases (CCEs), UDP-glycosyltransferases (UGTs), glutathione Stransferases (GSTs), ATP-binding cassettes (ABCs). We identified the protein families of all proteins by running InterProScan v. 5.36-75 (-appl Pfam oterms; Jones et al. 2014); on top of that, we ran a regional BLASTP against the UniRef50 database (ftp.uniprot. org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz;|G3, 2021, Vol. 11, No.Figure 4 FGFR Inhibitor medchemexpress Comparison of Lepidoptera genomes and inferred phylogenetic relationships. Shown is the ML phylogeny depending on 1367 single-copy BUSCOs (left, all nodes have 100 assistance unless otherwise noted). Quite a few detoxification gene members of 5 key detoxification families, P450s, CCEs, UGTs, GSTs, ABCs, are presented per species in a bubble plot generated with ggplot2.release version July 31, 2019, accessed August 20, 2019) employing an e-value cutoff of 1e-3. Depending on these annotations, genes have been selected to belong to any with the gene families of interest if it had a match to among the Uniref50 cluster terms or Pfam- orInterProScan identifiers (Supplementary Table S12). The number of detoxification gene members in the 5 most important detoxification households was plotted for every species in a bubble plot generated with ggplot2 (Wickham 2016; Figure 4).S. Simon et al.|Comparative analysis of Spodoptera-specific genesWe employed OrthoFinder v. 2.three.11 using default settings (Emms and Kelly 2015) to determine homologs within the Spodoptera clade. We incorporated the genome protein sequence files from three Spodoptera species: S. exigua (this study), S. litura [direct receival OGSv1 September 28, 2019 from authors (Cheng et al. 2017)] and S. frugiperda ( CNA0003276/Sf_20190612ynM_v1.pep, accessed September 20, 2019; Liu et al. 2019). Additionally, we included five closely associated but diverse Lepidoptera species: Heliothis virescens (ftp://ftp.ncbi. K63_refined_pacbio/GCA_002382865.1_K63_refined_pacbio_pro tein.faa.gz, accessed September 20, 2019; Fritz et al. 2018), Helicoverpa zea ( CIcsiro:23812v3, accessed August 21, 2019; Pearce et al. 2017), Helicoverpa armigera ( CIcsiro:23812v3, accessed August 21, 2019; Pearce et al. 2017), Trichoplusia ni ( gz, accessed September 20, 2019; Chen et al. 201