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).