Manual annotation of detoxification gene families
We manually annotated five detoxification gene families of cytochrome
P450 monooxygenase (P450s), glutathione S-transferase (GSTs),
carboxyl/cholinesterases (CCEs), UDP-glycosyltransferases (UGTs) and
ATP-binding cassette (ABC) transporters. We used the bioinformatic
pipeline BITACORA (Vizueta, Sánchez-Gracia, & Rozas, 2019) to conduct
HMMER v3.3 (Finn, Clements, & Eddy, 2011)and BLAST v2.2.31 (Altschul et
al., 1990) analyses under a full mode. Hits were filtered with a default
cut-off E-value of 10e-5. The HMMs of P450 were downloaded from Pfam
v32.0 (Sara El-Gebali et al., 2018), while other HMMs of detoxification
gene families were created by HMMER v3.3 (Finn et al., 2011). Orthologs
from Bombyx mori and D. melanogaster were used as
evidence. The annotated genes were further filtered manually based on
gene length and the presence of conserved domains. Genes with a length
shorter than 80 amino acids were removed. Orthologs were aligned with
the G-INS-I algorithm implemented in MAFFT v7.450 (Katoh & Standley,
2013). A neighbor-joining tree was constructed for each gene family
using MEGA7 (Kumar et al., 2016) with 500 bootstrap replicates.