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.