2.6 Phylogeny and comparative genomics
Orthologous groups were identified using the OrthoMCL pipeline (https://orthomcl.org/orthomcl/) (Li et al., 2003) with default parameters for M. dirhodum and nine other species, includingA. pisum (International Aphid Genomics Consortium., 2010), R. maidis (Chen et al., 2019),D. noxia (Nicholson et al., 2015), M. persicae (Mathers et al., 2017), Melanaphis sacchari (GCA_002803265.2),Nilaparvata lugens (Ma et al., 2021), Bemisia tabaci (Xie et al., 2017; Chen et al., 2019) and Apolygus lucorum (Liu et al., 2021). Drosophila melanogaster (Hoskins et al., 2015) was used as an outgroup. MAFFT (https://mafft.cbrc.jp/alignment/software/) (Katoh & Standley, 2013) was used to align each orthologous gene sequence with default parameters. RAxML (Stamatakis, 2014) was used to infer the maximum-likelihood tree with the best-fit substitution model and 1000 bootstrap replicates. Mummer (https://github.com/mummer4/mummer) was applied for a detailed collinearity analysis between the M. dirhodum and A. pisum genomes.