Genomic Signatures of Coevolution between Nonmodel Mammals and Parasitic Roundworms

Abstract

Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms and those of roundworm parasitism in general. The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts. The CTSZ and prolyl 4-hydroxylase subunit beta (P4HB) immunoregulatory proteins played a central role in protein interaction between mammals and parasitic roundworms. The gene tree comparison identified that seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host-parasite interaction. These coevolutionary proteins were particularly relevant to immune response. In addition, we found that the roundworms of both pandas exhibited higher proportions of metallopeptidase genes, and some positively selected genes were highly related to their larvae's fast development. Our findings provide novel insights into the genetic mechanisms of coevolution between nonmodel mammals and parasites and offer the valuable genomic resources for scientific ascariasis prevention in both pandas.

Keywords: coevolution; comparative genomics; pandas; parasitism.

Fig. 1.

Genome-wide phylogenetic tree, protease gene family composition, and annotated KEGG pathways for the secretomes of parasitic roundworms. (a) Phylogenomic tree, divergence times, and gene family expansion and contraction for five parasitic roundworms and three free-living nematodes. A yellow asterisk indicates a parasitic roundworm and its corresponding host, and a green asterisk indicates a free-living nematode. Two divergence times (red node) were used as the calibration points for estimating divergence times. (b) The proportions of different clans of proteases. The mixed type indicates the mixture of the cysteine, serine, and threonine catalytic types. (c) Annotated KEGG pathways for secretomes. The x-coordinate shows the types of annotated KEGG pathways, and the y-coordinate shows the number of genes for the corresponding KEGG pathways.

Fig. 2.

Positive selection related to the nutrient utilization and development of the roundworms from giant and red pandas, and positive selection and unique amino acid substitutions related to parasitism. (a) Two functional categories of positively selected genes in the roundworms from giant and red pandas. Trees 1, 2, and 3 indicate the first three positive selection analysis strategies, including both panda roundworms, only the giant panda roundworm, and only the red panda roundworm as the foreground branches, respectively. PSM, plant secondary metabolites. (b) In vitro development time of L1- and L2-stage larvae of three parasitic roundworms. The x-coordinate shows different temperature conditions and larval development stages, and the y-coordinate represents the development time (measured in minutes). A yellow asterisk indicates the host of the corresponding parasite. A lighter color in the column shows the fluctuation range of the development time. (c) GO biological process term enrichment of positively selected genes and unique amino acid substitutions related to parasitism. Trees 4 and 5 indicate the fourth and fifth positive selection analysis strategies, which both set all the parasitic roundworms as the foreground branches. Tree 4 only considered the positive selection of the most recent common ancestor lineage of five roundworms, and Tree 5 considered the positive selection of five roundworm lineages and their common ancestor lineages. Taking the nath-10 gene as an example, the arrow shows the enriched GO terms related to nath-10, and the multiple sequence alignments for 44 nematodes were ordered based on their phylogenetic relationships. Yellow represents free-living nematodes, and green represents parasites. Six amino acid substitutions were unique to all the parasites, with the number in the alignment being the location of unique amino acid substitutions.

Fig. 3.

PPI network between hosts and parasites. (a) The pipeline for building the host–parasite PPI network, the steps for predicting the secretome, and the homology-based PPI identification method. (b) Venn diagram for the number of PPIs in five host–parasite systems. The yellow asterisk indicates the host of the corresponding parasite. (c) The PPI network of the parasite protein CTSZ with host proteins. Darker orange indicates that this protein appears in all five systems, lighter orange indicates that this protein appears in more than one system, and white indicates that this protein appears in only one system. Fourteen host proteins displayed in squares were enriched in the MHC-II antigen presentation pathway. (d) The PPI network of parasite protein P4HB with host proteins. Darker blue indicates that the protein appears in all four systems, lighter blue indicates that the protein appears in more than one system, and white indicates that the protein appears in only one system. Thirty-six host proteins shown in squares were enriched in the integrin cell surface interaction pathway.

Fig. 4.

Species-level and gene-level phylogenetic relationships between hosts and roundworms, reflecting gene-level coevolution. (a) The species-level phylogenetic tree for hosts and roundworms. The yellow asterisk indicates the corresponding parasite. Symbol X shows inconsistency between two phylogenetic topologies. (b) Consistent gene trees for three pairs of interactive proteins, suggesting their molecular coevolution. The yellow asterisk indicates the corresponding parasite. The number on the branches represents the bootstrap value using Neighbor-Joining method.