Genomic Analysis Reveals the Role of New Genes in Venom Regulatory Network of Parasitoid Wasps

Abstract

New genes play a critical role in phenotypic diversity and evolutionary innovation. Parasitoid wasps, a highly abundant and diverse group of insects, parasitize other arthropods and exhibit remarkable evolutionary adaptations, such as evading host immune responses and exploiting host resources. However, the specific contributions of new genes to their unique traits remain poorly understood. Here, we identified 480 new genes that emerged after the Nasonia-Pteromalus divergence. Among these, 272 (56.7%) originated through DNA-mediated duplication, representing the largest proportion, followed by 77 (16.0%) derived from RNA-mediated duplication and 131 (27.3%) that arose de novo. Comparative analysis revealed that these new genes generally have shorter coding sequences and fewer exons compared to single-copy older genes conserved in the seven parasitoid wasps. These new genes are predominantly expressed in the reproductive glands and exhibit venom gland-biased expression. Notably, gene co-expression network analysis further identified that a new gene may act as a hub by interacting with older genes to regulate venom-related networks rather than directly encoding venom proteins. Together, our findings provide novel insights into the role of new genes in driving venom innovation in parasitoid wasps.

Keywords: evolution; gene regulatory network; new gene; parasitoid wasp; venom.

Figure 1

New genes identified in parasitoid wasps. (A) Distribution of new genes in the phylogenetic tree. Branches 0–6 were used as the distinct gene-age groups based on the synteny-based pipeline. Genes that emerged after Nasonia-Pteromalus split (branch 4–6) were identified as the new genes. Branches 4–6 (blue): Number of new genes. (B) Numbers and proportions of the new genes originated from DNA-mediated duplication, RNA-mediated duplication (retroposition), and de novo birth. (C) Stepwise origination process for an example of a de novo gene. The black bar represents a premature stop codon, the red arrow represents the frameshift insertion, and the grey bar indicates the frameshift deletion. Inserted bases are marked in red with their count shown. Deleted bases are marked in gray with their count shown. (D) The origination process for an example of retrotransposon. The blue or red box indicates exon.

Figure 2

The CDS length (A) and exon numbers (B) of three age groups (branch 0–1, branch 2–3, and branch 4–6). The white bar indicates the average of each age group. Wilcoxon’s test was used to calculate significance between age groups. p-value between age groups was calculated by Wilcoxon’s test, with significance levels indicated as follows: ** p < 0.01; *** p < 0.001.

Figure 3

Expression patterns of the new genes. (A) The log-scale expression of new gene and single copy genes for different tissues. The relative gene expression was calculated using log2 (median TPM + 1). (B) The tissue-specific score between new genes and old singleton genes. The black bar indicates the average. (C,D) Log2-based maximum expression levels across seven tissues and the number of tissues where genes were expressed (TPM > 1). Interquartile ranges are represented by black bars, while the violin curve illustrates the probability density of the data, with the median value indicated by a white dot. Genes were categorized into three groups based on their age identified in Figure 1A. p-value between age groups was calculated by Wilcoxon’s test, with significance levels indicated as follows: ns: not significant. *** p < 0.001.

Figure 4

Expression network of new and old genes across the different tissues. (A) Gene weight co-expression network. (B) The percentage of the new genes in the different modules. The vertical blue line represents the genome-wide percentage of the new genes (2.71%), and the proportion of new genes are indicated by blue points. (C) Heatmap of the tissue-specific index of the new genes across different modules. (D) The venom-related network was visualized, highlighting a hub gene with the highest degree of connections and its associated interactions. In the plot, orange node represents the core new gene, purple nodes represent venom-biased genes, and grey nodes represent non-biased genes. (E) Exon–intron structure of parental genes (blue) and new hub (orange) gene.