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 betweenB. schroederi and the other
three roundworms in the genome species are 35.37% (vsT. canis ), 43.86% (vsA. suum ), and 55.12% (vsP. 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 (A. Coghlan 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. S13a and S13b). Interestingly, a
similar expansion also appeared in the roundworm branch compared toM. hapla (Fig. S13c-d). For tissue development, we found that the
chitin-binding protein CPG-2 gene family issignificantly 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 (A. Coghlan et al., 2018).
In addition, according to the copy number statistics of expanded gene
families, the actin family is 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).