Genome of the parasitoid wasp Cotesia chilonis sheds light on amino acid resource exploitation

Abstract

Background: A fundamental feature of parasitism is the nutritional exploitation of host organisms by their parasites. Parasitoid wasps lay eggs on arthropod hosts, exploiting them for nutrition to support larval development by using diverse effectors aimed at regulating host metabolism. However, the genetic components and molecular mechanisms at the basis of such exploitation, especially the utilization of host amino acid resources, remain largely unknown. To address this question, here, we present a chromosome-level genome assembly of the parasitoid wasp Cotesia chilonis and reconstruct its amino acid biosynthetic pathway.

Results: Analyses of the amino acid synthetic pathway indicate that C. chilonis lost the ability to synthesize ten amino acids, which was confirmed by feeding experiments with amino acid-depleted media. Of the ten pathways, nine are known to have been lost in the common ancestor of animals. We find that the ability to synthesize arginine was also lost in C. chilonis because of the absence of two key genes in the arginine synthesis pathway. Further analyses of the genomes of 72 arthropods species show that the loss of arginine synthesis is common in arthropods. Metabolomic analyses by UPLC-MS/MS reveal that the temporal concentrations of arginine, serine, tyrosine, and alanine are significantly higher in host (Chilo suppressalis) hemolymph at 3 days after parasitism, whereas the temporal levels of 5-hydroxylysine, glutamic acid, methionine, and lysine are significantly lower. We sequence the transcriptomes of a parasitized host and non-parasitized control. Differential gene expression analyses using these transcriptomes indicate that parasitoid wasps inhibit amino acid utilization and activate protein degradation in the host, likely resulting in the increase of amino acid content in host hemolymph.

Conclusions: We sequenced the genome of a parasitoid wasp, C. chilonis, and revealed the features of trait loss in amino acid biosynthesis. Our work provides new insights into amino acid exploitation by parasitoid wasps, and this knowledge can specifically be used to design parasitoid artificial diets that potentially benefit mass rearing of parasitoids for pest control.

Keywords: Amino acid synthesis; Cotesia chilonis; Genome sequencing; Nutrition exploitation; Parasitoid wasps; Trait loss.

Fig. 1

Phylogenetic relationship among C. chilonis and other 12 parasitoid wasps. A A phylogenetic tree of C. chilonis with other parasitoid wasps based on 2179 single-copy orthologous genes by IQ-TREE maximum likelihood method and 1000 bootstrap replicates. All nodes received 100% bootstrap support. B A female C. chilonis attacking its host C. suppressalis and the cocoons of C. chilonis

Fig. 2

The amino acid biosynthetic pathway in the parasitoid wasp C. chilonis and its host C. suppressalis. The amino acid biosynthetic pathways were redrawn from the KEGG pathway, map01230. The pathway genes in gray are lost in both genomes of C. chilonis and C. suppressalis. The pathway genes in green are present in both genomes of C. chilonis and C. suppressalis. The pathway genes in orange are present in the genome of C. suppressalis but are lost in the genome of C. chilonis. The gene losses in the amino acid biosynthetic pathway of C. chilonis have disrupted the biosynthesis of ten amino acids (ASL-AA, Arg). However, the gene losses in the amino acid biosynthetic pathway of C. suppressalis have disrupted the biosynthesis of nine amino acids (ASL-AA), and the biosynthesis of these nine amino acids was thought to have been lost in the common ancestor of animals [25]. Gene copy number (GCN) of each pathway ortholog in C. chilonis and C. suppressalis was shown

Fig. 3

Rearing of C. chilonis with different rearing media in vitro. A In vitro rearing of C. chilonis. Five days after parasitism, larvae were put on the membrane of a Transwell chamber; then, the Transwell was placed in the well containing 250 μl of C. chilonis rearing medium so that the wasp larvae could reach the nutrients. B Survival rates of C. chilonis larvae developed on 13 different rearing media. Positive control: Grace’s Insect Medium, containing 20 amino acids (n = 30); negative control uses positive control medium minus the ten amino acids that C. chilonis cannot synthesize, ASL-AA, Arg, n = 30; single amino acid deficiencies use control media minus only one amino acid, indicated by “-” superscript, e.g., Gly deficiency (Gly^-) indicates excluding glycine only. The Gehan-Breslow-Wilcoxon test was used for survival rate statistical analyses, and the Benjamini-Hochberg method was used for multiple testing correction. The statistical results of pairwise group comparisons are indicated

Fig. 4

Parasitism by C. chilonis influences the free amino acid levels in host hemolymph. Free amino acid levels in host hemolymph were changed after parasitism. UPLC-MS/MS analysis was used. Host hemolymph was collected 3 days after parasitism. The detection for each treatment was repeated 10 times (n = 10). Student’s t-test was used for statistical analysis of amino acid changes. *p < 0.05, **p < 0.01

Fig. 5

Parasitism by C. chilonis suppresses the host’s amino acid biosynthetic pathways within 72 h after parasitism. A The amino acid biosynthetic pathways were modified from Fig. 2. The pathway genes in gray are lost in the genome of C. suppressalis. The pathway genes in green are present in the genome of C. suppressalis. Gene expression changes at 24 h (P1), 48 h (P2), and 72 h (P3) after parasitism were shown in three squares with different colors (gray, no significant expression change; green, significantly downregulated after parasitism, padj < 0.1). Gene set enrichment analyses (GSEA) showed that the genes in the amino acid biosynthetic pathways of C. suppressalis were largely downregulated at 24 h (B), 48 h (C), and 72 h (D) after parasitism. The top portion of the GSEA plot shows the running enrichment score for the gene set as the analysis walks down the ranked list. The middle portion of the GSEA plot reflects the positions of the members of the gene set in the ranked gene list. The bottom portion of the GSEA plot displays the value of the ranking metric along with the list. Three independent biological replicates of each sample for gene expression analyses were conducted (n = 3). Expression source data are included in Additional file 1: Table S8

Fig. 6

Parasitism by C. chilonis inhibits host amino acid utilization and activates host protein degradation within 72 h after parasitism. Gene set enrichment analyses (GSEA) showed that the genes in the amino acid metabolic pathways of C. suppressalis were largely downregulated at 24 h (A), 48 h (B), and 72 h (C) after parasitism. GSEA also revealed various expression changes of translation-related genes (GO: 0006412) at 24 h (D) and 48 h (E) after parasitism, and a significantly downregulated effect at 72 h (F) after parasitism. In addition, a significantly upregulated pattern of the host proteolysis-related gene set (GO: 0006508) at 72 h (I) after parasitism was found, but not at 24 h (G) or 48 h (H) after parasitism. Moreover, the expression of host storage protein genes was significantly inhibited within 48 h after parasitism (J). But we did not obverse statistical significantly differential gene expression at 72 h after parasitism. The gene expressions between parasitized hosts and controls at 24 h after parasitism (24hAP), 48 h after parasitism (48hAP), and 72 h after parasitism (72hAP) were compared respectively. The mean expression level (FPKM) of each treatment was used for heatmap plotting. Three independent biological replicates of each sample for gene expression analyses were conducted (n = 3). Expression source data are included in Additional file 1: Tables S9-S21