2.7 | Reconstruction of phylogeny and evolutional analysis among genomes from six nematodes
Genomes and annotation files of three roundworms parasitic on mammals (A. suum , T. canis and P. univalens ), one free-living nematode (C. elegans ) and one nematode parasitic on the root of a plant (M. hapla ) were download from NCBI or WormBase database (Table S10)(Michelle, Dubaj, Price, Daryl, & Hurd, 2019). The syntenic analysis both at whole-genome nucleotide-level and protein-level were performed by aligning 5 nematodes genomes to our assembled B. schroederi genome by using MCScanX(Y. Wang et al., 2012) software. Orthogroups among six nematodes are define using TreeFam (v4.0)(H. Li et al., 2006). Next, the protein sequences from each family were aligned using MUSCLE (v3.8.31)(Edgar, 2004) with default parameters. The conserved CDS alignments were extracted by Gblocks(Gerard & Jose, 2007). We select single-copy gene families to construct phylogenetic trees based on maximum likelihood using RAxML (v8.2.4)(Alexandros, 2014) with PROTCATGTR nucleotide substitution model with 500 bootstrap replicates.
Using the divergent time between C. elegans and A. suum,which was calculated based on fossil evidence, as the reference time points(Mcgill, Fitzpatrick, Pisani, & Burnell, 2017), we estimated the divergent time between each species by MCMCtree from the PAML (v4.8)(Bo & Yang, 2013) package with default parameters.