3.3 | Evolutionary and phylogenetic relationships among
six nematodes
We clustered the B. schroederi gene models with the genes from
five other nematode genomes (A. suum , P. univalens ,T. canis , C. elegans, and Meloidogyne hapla ; Table
S11). We found that the six
nematodes share 3,906 homologous gene families (Fig. 1c). In addition,
four roundworms show high consistency in the number of single-copy and
multi-copy genes (Fig. S11c). Collinearity results showed that although
several roundworms are closely related, collinearities among the genomes
are low (Fig. 1b). The proportions of collinearity between B.
schroederi and the other three roundworms in the genome species are
35.37% (vs T. canis ), 43.86% (vs A. suum ), and 55.12%
(vs P. univalens ), respectively, which indicate that genetic
differentiation among roundworms is considerable.
We used 2,451 single-copy genes shared within the six nematode genomes
to reconstruct a phylogenetic tree (Fig. 1d). The relationships among
the six nematodes in the phylogenetic tree are consistent with a
previous study(International et al., 2018). B. schroederi is
closely related to A. suum and P. univalens . According to
the TimeTree(Hedges, 2011) database and fossil evidence from A.
suum and C. elegans (Mcgill et al., 2017), we estimated the
divergence time to approximately 400-269 million years ago (Mya), and
the divergence time between the four roundworms is approximately 160-26
Mya (Fig. 1d). Among the four roundworms, T. canis was identified
as the earliest branch to the other three roundworms (approximately 134
Mya).
3.4 | Expanded and contracted genes inAscariasis
Compared with C. elegans and M. hapla , a large number of
genes have been lost or contracted in the branch of roundworms (Fig.
2a). Specifically, we found that 563 gene families are significantly
contracted (P <0.05), with an average loss of 1.61 genes
in each family (Table S12). However, roundworms also show significant
expansion in 29 gene families (P <0.05). We focused on
the changes in gene number related to free life and those related to
parasitic life in nematodes. For both the expanded and contracted gene
families, KEGG enrichment analysis showed that pathways related to
tissue development, metabolism and environmental information processing
had undergone significant changes (Fig. S12a and S12b). Interestingly, a
similar expansion also appeared in the roundworm branch compared toM. hapla (Fig. S12c-d). For tissue development, we found that theCPG-2 gene family is significantly expanded in the roundworm
branch (P <0.01). In addition, a significant expansion
of the tight junctions (ko04530), phagosome pathway (ko04145) and Rap1
signaling pathway (ko04015) was observed (P <0.01; Fig
2a). In relation to self-defense, consistent with a previous study, we
observed an expansion of the chymotrypsin/elastase inhibitor gene
family, which may be related to a protection of roundworms from host
proteases(International et al., 2018). In addition, according to the
copy number statistics of expanded gene families, the actin family was
significantly expanded among all four roundworms (Fig. 2b). GO
enrichment analysis showed that the genes related to nematode behavior
and biological adhesion accounted for the most significant difference
among all gene families exhibiting expansions in roundworms (Fig. 2c).