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.