Comparative genomic analysis reveals the genetic basis of the environmental adaptability of Propylea japonica

Abstract

Background

Propylea japonica is a widely distributed natural enemy insect that preys on aphids, whiteflies, and other pests. Owing to its exceptional environmental adaptability, this species serves as an effective biological control agent. However, the molecular mechanisms underlying its environmental adaptation remain poorly understood.

Results

Phylogenetic analysis revealed that Coccinellidae diverged from other Coleoptera approximately 194.88 million years ago, and P. japonica and Harmonia axyridis diverged approximately 91.94 million years ago. Collinearity analysis revealed significant fission and fusion events during the chromosomal evolution of P. japonica. Notably, comparative genomic analysis revealed the following five potential key mechanisms underlying the environmental adaptability of P. japonica: (1) sensory specialization: odorant-binding proteins and water sensation genes may enhance prey and water detection; (2) genome stability: histone-mediated chromatin resilience may maintain genome integrity and developmental plasticity under stress; (3) energy trade-offs: prioritizing detoxification or immunity under toxin exposure may reduce the amount of resources allocated to growth or reproduction, enhancing niche adaptation; (4) developmental robustness: juvenile hormone signaling and embryonic development pathways potentially ensure developmental stability; (5) dispersal adaptation: enhanced development of wings and flight muscles and chitinase activity may facilitate colonization to escape extreme climates or resource scarcity.

Conclusions

Through comparative genomic analysis, this study provides insights into the divergence history of Coleoptera and reveals a dynamic pattern of chromosomal evolution in P. japonica, clarifying the genetic basis of its environmental adaptation. Future studies should prioritize the functional validation of candidate genes linked to these five key mechanisms to better elucidate their specific contributions to environmental adaptation. This work advances the molecular understanding of ecological adaptation in predatory insects, providing actionable perspectives for optimizing biocontrol strategies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-025-12330-1.

Introduction

Coleoptera, the most diverse group of insects, has significant ecological and economic value. Species within this order play diverse ecological roles, including phytophagous, predatory, and saprophagous [1, 2]. Among them, ladybird beetles (Coccinellidae), comprising more than 6,000 described species worldwide, occupy a prominent position [3]. Predatory members of the subfamily Coccinellidae serve as crucial natural enemies, providing irreplaceable benefits in the biological control of agricultural pests [4].

Propylea japonica is a widely distributed predatory insect that feeds on aphids, whiteflies and other small pests [1, 5]. This species exhibits remarkable ecological adaptability, including tolerance to hunger, high temperature, and pesticides, as well as high reproductive capacity under suboptimal dietary conditions [6, 7]. These characteristics establish P. japonica as a crucial species for integrated pest management in agricultural ecosystems. Previous studies have shown that the pesticide resistance of P. japonica is linked to elevated activity of detoxification enzymes, including glutathione S-transferase, carboxylesterases, and cytochrome P450 monooxygenase [8]. Furthermore, under high temperature stress, antioxidant enzymes play a critical role in mitigating oxidative damage [9]. At the omics level, a chromosomal-level genome assembly of P. japonica has been constructed, in which genes encoding proteins involved in environmental adaptation, such as cytochrome P450 genes, have been identified [10]. Dynamic transcriptomic analysis revealed genes related to juvenile hormone (JH) synthesis and the nutrient-sensing signaling pathway, which are involved in reproductive regulation in P. japonica [11]. Extensive population genomic investigations have revealed the patterns of genetic variation, population differentiation, and evolutionary trajectory of this species [12]. Despite these advances, the genetic mechanism underlying the exceptional ecological adaptability of P. japonica remains unclear, hindering a deeper understanding and optimal utilization of its biological traits.

With the rapid advancement of genomics, comparative genomic analysis has become a powerful tool for exploring the ecological adaptation of species. For instance, comparative genomic analysis of Spodoptera frugiperda and 45 other species of Lepidoptera revealed that significant expansions in gene families associated with growth, reproduction, stress response, and immune function are key contributors to its environmental adaptation [13]. Similarly, parasitic lice from different hosts also exhibited expansions in conserved gene families related to digestion, detoxification, and immunity, a pattern observed to underscore their adaptive evolution during host transitions [14]. In predatory ladybirds, comparative analysis shows that expansions in chemosensory, digestive, and immune-related gene families underpin the specialized adaptation of Novius pumilus to a predatory lifestyle [15]. Collectively, these studies confirm that expansions in chemosensory, digestive, detoxification, and immune-related gene families serve as fundamental genomic mechanisms driving adaptive evolution and ecological success.

Recent advances in genome sequencing have enabled the assembly of high-quality genomes for an increasing number of Coleoptera species, offering an unprecedented opportunity to investigate environmental adaptation mechanisms in P. japonica. In this study, we conducted a comparative genomic analysis of seven species of Coleoptera. Through comparative phylogenetic analysis of Coleoptera species, we elucidated the divergence chronology of Coleoptera. Combined with interspecific chromosomal collinearity analysis between P. japonica and related taxa, this study further delineated the chromosomal evolutionary trajectory of P. japonica. Through the identification of species-specific gene families, the analysis of gene family expansion/contraction patterns, and the detection of positively selected genes, we aim to: (1) elucidate the molecular basis of environmental adaptation in P. japonica, (2) provide genomic evidence for the ecological adaptation mechanisms of predatory ladybird beetles, and (3) provide a theoretical foundation for optimizing agricultural pest control strategies.

Materials and methods

Genome data collection

In this study, we performed a comparative analysis of the genomes of seven Coleoptera species and one Neuroptera species. These seven Coleoptera species belong to six families within Coleoptera, including P. japonica and Harmonia axyridis (Coccinellidae), Brassicogethes aeneus (Nitidulidae), Phyllotreta striolata (Chrysomelidae), Tribolium castaneum (Tenebrionidae), Holotrichia oblita (Melolonthidae) and Pyrocoelia pectoralis (Lampyridae). In addition, Chrysopa pallens (Neuroptera: Chrysopidae) was used as the outgroup. All the genomes were downloaded from the National Center for Biotechnology Information (NCBI) database, except for those of H. axyridis (InsectBase database). Refer to 1 for the genome data download web links of these 8 species (Table 1).

Table 1.

Genome information of eight species

Species	Genomes	BioProject Accession
P. japonica	https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_013421045.1/	PRJNA498898
H. axyridis	http://insect-genome.com/Haxy/	PRJNA579455
B. aeneus	https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_921294245.1/	PRJEB48953
P. striolata	https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_918026865.1/	PRJEB47901
T. castaneum	https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002335.3/	PRJNA12540
H. oblita	https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_023690525.1/	PRJNA812706
P. pectoralis	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/036/250/285/GCA_036250285.1_FXH_PpeL_2.0/	PRJNA1014999
C. pallens	https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_020423425.1/	PRJNA685652

Gene family identification

To identify gene families, we extracted the protein sequences encoded by the longest transcripts of each gene were extracted from eight species. OrthoFinder v2.4.0 [16] was used to cluster homologous genes into families by employing DIAMOND for pairwise sequence comparison with an E-value cutoff of 0.001. The resulting gene families were functionally annotated using the Panther V15 database [17]. In addition, P. japonica -specific gene families were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses using clusterProfile v3.4.4 [18]. This method implemented hypergeometric test algorithms, and the q-value (false discovery rate, FDR) was calculated to adjust the p- value using the R package (https://github.com/StoreyLab/qvalue). For both the GO enrichment and KEGG pathway analyses, we chose q < 0.05 was chosen as the significance threshold. The figure was created by https://www.bioinformatics.com.cn (last accessed on 9 June 2025).

Phylogenetic analysis

Based on 478 single-copy orthologous gene sequences, the phylogenetic relationships among the 8 species were reconstructed. Protein sequences were aligned using MAFFT v7.205 with the parameters ‘--localpair --maxiterate 1000’ [19]. Poorly aligned or highly divergent regions were trimmed using Gblocks v0.91b (-t = p, -b5 = h) [20], and the remaining high-quality alignments were concatenated into a supergene matrix. A phylogenetic tree was constructed using IQ-TREE v2.2.0 under the maximum likelihood (ML) framework [21]. The best-fit substitution model (LG + F + I + G4) was selected via ModelFinder [22]. Branch support was assessed with 1000 ultrafast bootstrap replicates. Divergence times were estimated using the MCMCTREE module in PAML v4.9i [23] with fossil calibrations obtained from the TimeTree database (http://www.timetree.org/): C. pallens - T. castaneum, 258.4–342.8 million years ago (Mya); H. oblita - T. castaneum, 233.4–238.4 Mya; P. striolata - T. castaneum, 152.3–236.2 Mya. The analysis first computed gradients and Hessian matrices, followed by maximum likelihood estimation of divergence time under a correlated molecular clock model and Jukes–Cantor (JC69) nucleotide substitution model. We performed two independent replicates to confirm the consistency of the results (correlation between replicates = 1). The Markov chain Monte Carlo (MCMC) settings were as follows: burn-in: 5,000,000 iterations, sampling frequency: every 30 iterations, and total number of samples: 10,000,000. Finally, time-calibrated trees were visualized using MCMCTreeR v1.1 [24].

Chromosome collinearity analysis

We performed a genome collinearity analysis between P. japonica and six other species using a multistep approach. Owing to the non-chromosomal level of the H. axyridis genome, no chromosomal collinearity analysis was conducted. First, similar gene pairs were identified by aligning the gene sequences of two species using DIAMOND v0.9.29.130 [25] (e-value < 1e-5 and C score >0.5), and the C score was filtered using JCVI v3.5.2 [26]. MCScanX with the parameter (-m 15) [27] was then employed to identify collinearity blocks based on chromosomal adjacency from the GFF3 annotations. Finally, the genome-wide collinearity patterns of P. japonica and its six closely related species were visualized using JCVI v3.5.2, providing new insights into chromosome evolution relationships across these species.

Gene family expansion analysis

Using the identified gene families and the time-calibrated phylogenetic tree of eight species, we analyzed gene family dynamics with CAFE v4.2 [28]. The birth-death model was applied to simulate the gain and loss of gene families across the phylogeny. A significant expansion or contraction was defined as having both family-wide p-values and Viterbi p-values below the threshold of 0.05. For P. japonica, all significantly expanded gene families (p-value ≤ 0.05) were functionally characterized via GO and KEGG pathway enrichment analysis using clusterProfiler v3.4.4 [18]. This method implemented hypergeometric test algorithms and the q- value (FDR) was calculated to adjust the p- value using the R package (https://github.com/StoreyLab/qvalue). For both the GO enrichment and KEGG pathway analyses, q < 0.05 was chosen as the significance threshold. The figure was plotted by https://www.bioinformatics.com.cn (last accessed on 9 June 2025).

Positive selection analysis

To detect signatures of positive selection in P. japonica, we analyzed single-copy orthologous genes across five closely related species, including H. axyridis, P. japonica, T. castaneum, B. aeneus and P. striolata, based on the phylogenetic tree to estimate the dN/dS ratio (ω) of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitutions using the PAML v4.9i package [23]. Protein sequences were first aligned with MAFFT v7.205 [19] using the parameter ‘--localpair --maxiterate 1000’, followed by codon-based nucleotide alignment conversion using PAL2NAL. We then performed selection analysis using CodeML (PAML v4.9i) with the F3 × 4 codon frequency model under a branch-site framework. Likelihood ratio tests (LRTs) were performed between Model A (which allows sites with ω >1 on the foreground branches) and a null Model (which does not allow ω >1 at any site) using the chi2 program in PAML. A significant difference was inferred for p-values < 0.05. The Bayes empirical Bayes (BEB) method was then employed to identify sites under positive selection, with posterior probabilities >0.95 considered significant. Genes containing such sites were identified as having undergone significant positive selection. Finally, genes under significant positive selection were functionally characterized via GO and KEGG enrichment analyses using clusterProfiler v3.4.4 [18]. This method implemented hypergeometric test algorithms and the q-value (FDR) was calculated to adjust the p-value using the R package (https://github.com/StoreyLab/qvalue). In GO and KEGG enrichment analyses, we retained p < 0.05 as the significance cutoff despite the adjusted p- values (q- values) not meeting the statistical significance threshold after multiple testing correction. This decision was based on the potential biological relevance of systematic association patterns in P. japonica’s environmental adaptation. The figure was plotted by https://www.bioinformatics.com.cn (last accessed on 9 June 2025).

Results

Identification and comparison of gene families and genes

We analyzed the genomes of seven Coleoptera species and one Neuroptera species. Using OrthoFinder v2.4.0 [16], 96,722 genes (78.4% of the total) were clustered into 16,923 gene families, among which 478 were identified as single-copy gene families. The analysis revealed that H. oblita had the greatest number of multiple-copy gene families (4434) but the lowest number of single-copy gene families (3945) among all eight species (Fig. 1a; Table S1). In contrast, compared with P. japonica (6359), H. axyridis had more single-copy genes (7174), while the latter species had more multiple-copy genes (Fig. 1a; Table S1). Notably, while P. japonica possessed the second-largest number of multicopy genes (8796) after H. oblita, the latter exhibited the greatest number of species-specific gene families (910) among the 2239 gene families conserved across all the species (Fig. 1b). A comparison between invasive H. axyridis and native P. japonica revealed a significantly greater number of species-specific gene families in the former (844 vs. 368) (Fig. 1b), a finding consistent with their distinct ecological adaptations.

Fig. 1.

Gene family clustering and P. japonica specific GO enrichment analysis. a Gene families and genes across eight insect species. b Flower plot of species-specific families and common gene families of the eight species. Numerical labels below species names represent gene numbers within species-specific gene families. c GO enrichment analysis of P. japonica-specific gene families (q < 0.05; top 10). The circle size represents the gene number, and the color indicates the q value (adjusted p value). BP: Biological Process. CC: Cellular Component. MF: Molecular Function. d Xenobiotic detoxification-related GO terms and genes in P. japonica-specific gene families

We subsequently performed GO enrichment and KEGG pathway analyses on the 368 P. japonica-specific gene families (q < 0.05). GO analysis revealed significant enrichment in several key functional categories (Table S2; Fig. 1c), including: genome stability maintenance (e.g., DNA integration, DNA recombination), transcriptional regulatory mechanisms (RNA surveillance, RNA‒DNA hybrid ribonuclease activity), response to mechanical stimulus, larval behavior, xenobiotic detoxification (e.g., ATP-binding cassette (ABC) transporter complex) and odorant binding. Notably, RNA surveillance (rich factor: 16.25) and RNA‒DNA hybrid ribonuclease activity (rich factor: 15.24) were the most enriched, suggesting that sophisticated transcriptional regulation may be crucial for the species-specific evolution of P. japonica. Additionally, recurrent enrichment of mechanical stimulus response and larval behavior terms was linked to four pickpocket (PPK) protein-encoding genes (Fig. S1), suggesting the involvement of a shared molecular mechanism. Notably, several enriched terms, such as oxidation‒reduction process, drug transport, ABC transporter complex, iron ion binding, heme binding, and oxidoreductase activity acting on paired donors, were associated with 16 CYP450 genes and 4 multidrug resistance protein (MRP/ABCC) genes (Fig. 1d, Table S3), highlighting their potential role in xenobiotic detoxification in P. japonica.

KEGG pathway analysis indicated enrichment primarily in herpes simplex virus 1 infection (ko05168) and terpenoid backbone biosynthesis (ko00900) (q < 0.05). Enrichment in viral interaction pathways may reflect evolutionary adaptation to pathogen challenges.

Phylogenetic relationships and chromosome evolution of Coleoptera

We constructed a maximum-likelihood phylogenetic tree using 478 single-copy orthologous protein sequences from eight species, with C. pallens (Neuroptera) designated as the outgroup (Fig. 2a). The tree topology revealed six coleopteran families as monophyletic clades, all with high statistical support (ultrafast bootstrap values = 100%) (Fig. S2). Specifically, P. japonica clustered closely with H. axyridis (Coccinellidae), while P. striolata and B. aeneus formed a distinct sister lineage. The remaining three coleopteran families each occupied separate, well-supported branches. A time-calibrated phylogenetic tree indicated that Chrysopidae diverged from Coleoptera approximately 301.65 Mya (95% HPD = 268.29‒343.14 Mya) and that Coccinellidae was separated from other coleopteran families approximately 194.88 Mya (95% HPD = 182.11‒210.74 Mya), and the split between P. japonica and H. axyridis occurred approximately 91.94 Mya (95% HPD = 55.35‒132.25 Mya) (Fig. 2a).

Fig. 2.

Phylogenetic reconstruction and chromosomal collinearity analysis of P. japonica and related Coleoptera species. a Time-calibrated phylogenetic tree of eight species. C. pallens as the outgroup. The estimated divergence times are indicated by black numbers at each node. b Chromosomal collinearity of P. japonica, P. pectoralis and H. oblita. c Chromosomal collinearity of P. japonica, T. castaneum and B. aeneus

Furthermore, collinearity analysis among the five Coleoptera species and the outgroup revealed complex chromosomal evolution in P. japonica. Analysis revealed that the chr1 and X chromosome in C. pallens are homologous to chr7 and chr9 in P. japonica, respectively (Fig. S3). In P. pectoralis, chr3 was split into parts of chr1 and chr7 in P. japonica (Fig. 2b). Further rearrangements include the fusion of chr6 and chr7 of H. oblita into chr5 of P. japonica, whereas chr8 of H. oblita aligned to chr8 and chr9 in P. japonica (Fig. 2b). In P. pectoralis, chr6 and chr8 fused into chr0 in P. japonica, which corresponds to single chromosome in H. oblita, T. castaneum, and B. aeneus, respectively (Fig. 2b, c). Although T. castaneum and B. aeneus exhibit high collinearity with P. japonica, their chr2 and chr4 split into chr4 and chr6 in P. japonica, whereas their chr6 and chr9 split into chr8 and part of chr9 in P. japonica (Fig. 2b, c). Additionally, chr10 and chr11 of B. aeneus fused into a segment of chr3 in P. japonica, suggesting that B. aeneus underwent chromosome fission events (Fig. 2c). Despite sharing a clade with B. aeneus, P. striolata exhibits markedly lower collinearity with P. japonica, retaining homology only between chr11/chr10 and chr0/chr9 (Fig. S4). Overall, P. japonica maintains broad collinearity with other Coleoptera species but has undergone extensive chromosomal fission and fusion, reflecting dynamic genome evolution. These findings underscore the role of fission/fusion events in shaping structural diversity across Coleoptera genomes.

Gene family expansion analysis

To investigate gene family dynamics across the eight species, we integrated the results of gene family identification with a time-calibrated phylogenetic tree. On the base of ancestral reconstruction, we identified gene families that had undergone significant expansion (p < 0.05) (Fig. 3a). The results indicate that all the examined species have experienced varying degrees of significant gene family expansion throughout their evolutionary histories. Within Coleoptera, expansion events consistently outnumbered contraction events across all lineages. Compared with other Coleoptera families, Coccinellidae showed 23 significantly expanded and 11 contracted gene families. Among the individual species, H. oblita exhibited the most dramatic expansion (83 gene families). In H. axyridis, there were showed 81 expanded and 30 contracted gene families, whereas in P. japonica, there were 72 expanded gene families and 20 contracted gene families. The significant expansions in lady beetle species (H. axyridis and P. japonica) likely reflect specific ecological adaptations.

Fig. 3.

Gene family evolution and functional enrichment of the expanded gene families in P. japonica. a Gene family expansion and contraction analysis of the eight insect species. Gene family dynamics are represented by (1) branch-specific numbers of significantly expanded (red) and contracted (blue) gene families and (2) pie charts at each node showing the proportion of expanded (red) versus contracted (blue) gene families. b GO enrichment analysis of significantly expanded gene families of P. japonica (q < 0.01). The top 20 BP and MF terms are shown. The circle size represents the gene number, and the color indicates the q value (adjusted p value). c KEGG pathway analysis of significantly expanded gene families of P. japonica (q < 0.01). The colors indicate KEGG pathway categories: orange (metabolism), green (environmental information processing), blue (cellular processes), and purple (organismal systems)

We subsequently performed GO and KEGG enrichment analyses on the 72 significantly expanded gene families in P. japonica (q < 0.01). These gene families presented multidimensional evolutionary features in the GO enrichment analysis (Table S4; Fig. 3b), with significant enrichment in the following functional categories: genomic stability maintenance (DNA integration), chromatin remodeling (e.g., chromatin assembly, nucleosome), hormone metabolism (e.g., hormone biosynthetic process), primarily Juvenile hormone acid O-methyltransferase (JHAMT), reproductive behavior (courtship behavior), lipid metabolism, xenobiotic detoxification (e.g., toxin metabolic process), digestion (e.g., lipase activity), linked to proteases and lipases, and the innate immune response (e.g., regulation of antifungal peptide production), predominantly associated with toll-like receptor 3. Additionally, significant enrichment was observed for odorant-binding proteins (odorant-binding) and histone family genes. Notably, 24 enriched GO terms, including highly enriched chromatin assembly, nucleosome organization, and DNA packaging complex formation, were functionally associated with the histone family (Table S5). In total, 81 histone genes were detected, including 20 histone H2A genes, 21 histone H2B like genes, 24 histone H3 genes, 1 histone H3.3 gene and 16 histone H4 genes (Table S6). Furthermore, many genes associated with xenobiotic detoxification were identified, predominantly comprising 45 CYP450s, 13 UGTs, 9 CarEs, and 4 GSTs (Table S7). Notably, all 45 CYP450 genes were annotated to both iron ion binding and heme binding terms, highlighting their central role in detoxification.

KEGG analysis revealed enrichment in metabolic regulation and environmental adaptatiion pathways (Fig. 3c), including: energy metabolism (e.g., ether lipid metabolism and glycolysis/gluconeogenesis), xenobiotics detoxification (e.g., metabolism of xenobiotics by cytochrome P450), amino acid metabolism (e.g., Histidine metabolism), insect hormone biosynthesis, digestive system (e.g., salivary secretion, lysosome). The results of KEGG pathway analysis confirmed the results of the GO enrichment analysis.

Positively selected genes in Propylea Japonica

To identify positively selected genes (PSGs), we analyzed single-copy gene families from five representative Coleoptera species (H. axyridis, P. japonica, T. castaneum, B. aeneus, and P. striolata) within the same major clade of the evolutionary tree using the CodeML module in PAML [23]. This analysis identified 181 significant PSGs in P. japonica. Subsequent GO and KEGG enrichment analyses of these PSGs (p < 0.05) revealed significant functional categories and pathways.

GO enrichment analysis indicated that PSGs contribute to multifaceted environmental adaptations (Fig. 4a), with significant enrichment in the following functional categories: cell polarity and cell junction (e.g., cell shape regulation and cell junction assembly), developmental processes (e.g., tube development), cuticle remodeling (e.g., chitinase activity), muscle function (e.g., sarcomere organization), signal transduction (e.g., synaptic vesicle exocytosis9), and hormone response (sterod hormone receptor activity). Of particular interest, 11 cell junction-related GO terms were enriched, with four recurrently associated core genes (EVM0006964.1, EVM0013314.1, EVM0007352.2, and EVM0003891.1) (Fig. 4b, Table S8). Furthermore, developmental regulation was associated with multiple GO terms, with periodic partitioning (rich factor: 14.59) being the most significantly enriched (Fig. S5). KEGG analysis revealed the involvement of PSGs in metabolic regulation (fatty acid metabolism and fructose and mannose metabolism), axon guidance, and signaling pathways (phosphatidylinositol signaling system) (p < 0.05). The functional profiles of the positively selected genes converge on key processes such as developmental plasticity, metabolic homeostasis, and signal transduction. This implies that evolutionary adaptations in these genetic pathways may collectively underpin the broad environmental adaptability of P. japonica.

Fig. 4.

GO enrichment analysis of positively selected genes in P. japonica (p < 0.05) (a) and cell junction-associated GO terms (b). The circle size represents the gene number, and the color indicates the p value

Discussion

Recent advancements in chromosome-level genome assembly have considerably facilitated comparative genomic analysis across insect species, significantly enhancing our understanding of their ecological adaptations and evolutionary processes [29]. In this study, we performed a comparative genomic analysis of eight insect species to reconstruct the evolutionary history of Coleoptera, elucidate the chromosomal evolutionary dynamics in P. japonica, and identify key genes associated with environmental adaptation. Our findings thus provide novel molecular insights into the evolutionary adaptation mechanisms of Coccinellidae predators in agricultural ecosystems.

Phylogenetic divergence history and chromosome evolution of coleoptera

The time-calibrated phylogeny indicated that Coleoptera and Neuroptera diverged approximately 301.65 Mya, aligning with previous estimates of beetle origins at ~ 297 Mya [30]. Within Coleoptera, Coccinellidae diverged from other families approximately 194.88 Mya, a timeframe that is between the estimates of 236.21 Mya [10] and 142 Mya [3]. Phylogenetic analysis confirmed a close evolutionary relationship between P. japonica and H. axyridis, with divergence during the Turonian stage of the Late Cretaceous (91.94 Mya). This divergence postdates the split with T. castaneum, which is consistent with established patterns [3, 15].

Chromosome-level comparisons revealed extensive fission/fusion events in P. japonica (n = 10), showing limited collinearity with P. striolata and C. pallens but conserved collinearity with B. aeneus, T. castaneum, H. oblita, and P. pectoralis. Notably, the X chromosome of C. pallens corresponds to chr9 of P. japonica, suggesting that chr9 may function as a sex chromosome in this species. Although B. aeneus and P. striolata are relatively closely related, their collinearity with P. japonica differs substantially. Only chr10 and chr11 of P. striolata show collinearity with those of P. japonica. These patterns suggest that B. aeneus preserves a chromosomal architecture closer to the P. japonica ancestral state, whereas P. striolata likely underwent significant rearrangements after speciation. Furthermore, while previous studies have identified chromosomal fusion events in H. axyridis [31], our results show both fusion and fission events in the chromosome of P. japonica. Although a direct synteny analysis between these two ladybird species was not conducted in this study, the observed presence of fusion events in both predators implies that chromosomal fusion could represent a notable mechanism in the chromosomal evolution of predatory ladybirds (Coccinellidae).

Sensory specialization for ecological niche adaptation

Olfaction is a critical mechanism for environmental communication in insects and governs essential behaviors such as development, foraging, mating, reproduction, and hazard avoidance [32–34]. A genomic analysis of P. japonica identified a notable expansion in odorant-binding proteins (OBPs), with 14 and 13 OBPs enriched within its species-specific and significantly expanded gene families, respectively. Given that OBPs are involved in predatory adaptation in predatory ladybirds, N. pumilus [15], it is likely that they also play an important role in prey adaptation in P. japonica, thus contributing to its ecological success. We further identified the osmosensitive ion channel ppk28 and ppk28-like as shared molecular mediators of the mechanical stimulus response and larval behavior regulation. Mechanical stimuli induce behavioral transitions in insect larvae, enabling rapid adaptive responses [35]. In Drosophila, ppk28 regulates drinking behavior [36] and coordinates metabolic homeostasis through adipokinetic hormone signaling, thus influencing lifespan [37]. It is therefore plausible that the ppk28 orthologs in P. japonica regulate analogous water-sensing functions. In conclusion, the dual specialization of olfaction and water sensation may optimize both predatory efficiency and survival adaptation, potentially driving the ecological success of P. japonica in fluctuating environments.

Xenobiotic detoxification and immune adaptations

Although P. japonica is an effective biological control agent, its performance in the field is often limited by prey scarcity and abiotic stressors, especially pesticide exposure. Our genomic analysis revealed that this species possesses a robust detoxification system characterized by the expansion of xenobiotic metabolizing gene families (e.g., 45 CYP450s, 13 UGTs, 9 CarEs, and 4 GSTs) as well as species-specific genes such as 16 CYP450s and 4 MRP/ABCC transporters. Given the established roles of these enzymes and transporters in toxin metabolism [38–40] and efflux [41, 42], their genomic abundance suggests a strong genetic basis for pesticide resistance in P. japonica. The expansion of detoxification gene families is commonly observed in insects, ranging from phytophagous pests [43, 44] to herbivorous and predatory ladybirds [3, 45], facilitating their adaptation to environmental toxins. Despite variations in the specific genes that have expanded across species, this recurrent trend highlights a convergent evolution strategy. Moreover, these gene families often play pleiotropic roles, contributing not only to detoxification but also to other critical biological functions. For example, CYP4C1 regulates thermal adaptation in Bemisia tabaci [46], esterase FE4 promotes oxidative stress resistance [47], and CYP6k1 acts as an odorant-degrading enzyme in Diaphorina citri [48]. This multifunctionality may not only underscore the strong xenobiotic resistance of P. japonica, but also highlight the evolutionary innovation of its detoxification system in adapting to agricultural ecosystems.

Furthermore, the expansion of the detoxification metabolism-related gene family underlies the chemical resistance of P. japonica, whereas the parallel expansion of the immune-related gene family enhances its defense against environmental pathogens. Enhanced immune competence has been shown to facilitate invasion and colonization in species such as H. axyridis [49]. In P. japonica, this capacity may be linked to the reinforced Toll pathway, a key NF-κB signaling cascade. Its efficacy is potentially enhanced through mechanisms such as TLR3-mediated NF-κB activation [50]. Therefore, the expanded immune and detoxification capacities collectively provide a dual adaptive advantage for P. japonica, enabling it to tolerate both chemical and biological stressors and serve as a mechanistic basis for its establishment and dispersal in heterogeneous environments.

Histone-Mediated genome stability and epigenetic regulation

Histones, as fundamental chromatin components, play pivotal roles in maintaining genome stability. In P. japonica, we observed significant expansion of both replication-dependent (RD) histone genes (H2A, H2B-like, H3, H4) and the replication-independent (RI) variant H3.3. A growing body of evidence points to histone gene family expansion as a genomic adaptive feature in insects that plays a dual role in maintaining genomic integrity and regulating the phenotypic traits critical for growth and development in complex environments. Specific expansions associated with its growth and reproduction have been reported in the parasitoid wasp Nasonia vitripennis [51] and S. frugiperda [13]. In contrast, although no significant expansion has occurred in Hylurgus ligniperda, its histone genes still contribute to environmental adaptation by participating in hormone biosynthesis and longevity regulation [52]. Additionally, histone homeostasis is crucial for cell cycle progression [53], transcription [54], genome stability [55] and chromatin dynamics [56]. Furthermore, histone acetylation and methylation dynamically regulate chromatin states, influencing insect reproductive diapause [57, 58]. In conclusion, the expansion of histone gene families may represent a widespread adaptive strategy for insects to maintain genome stability in response to environmental challenges. The specific expansion observed in P. japonica suggests that enhanced epigenetic plasticity and rapid evolutionary potential are indispensable for the ecological success of a polyphagous predator.

Developmental plasticity and flight adaptation

As an ecologically crucial predator, P. japonica likely evolved robust developmental mechanisms to cope with environmental stressors. This inference is supported by the significant enrichment of positively selected genes in functional terms related to cell junction and developmental regulation. Four key proteins are associated with cell junction terms: tight junction protein ZO-1, amalgam, neurotrimin, and cadherin-86 C-like. These four proteins play central roles in embryogenesis [59], neural development [60], and flight muscle formation [61]. At the developmental regulatory level, we identified several PSGs, such as serine protease nudel-like, labial, apterous, sister of odd and bowel (sob), homeobox protein slou (slouch) and troponin T. These genes govern fundamental developmental processes, such as the development of wings [62, 63] and flight muscles [64]. Notably, two positively selected chitinases (chitinase 2 and chitinase 6) essentially contribute to insect wing cuticle formation [65, 66]. These PSGs may maintain developmental stability and optimize the flight performance of P. japonica by regulating embryonic patterning, wing morphogenesis and the function of flight muscles, reinforcing its ecological role as a mobile predator.

Additionally, a JHAMT gene, a key enzyme in the final step of JH biosynthesis, was identified among the significantly expanded gene family of P. japonica. Knockdown of JHAMT disrupts larval development in Bactrocera dorsalis [67]. Notably, the downregulation of the expression of JHAMT during prolonged flight in Locusta migratoria implies its role in the balance between flight and reproduction [68]. Given that JH signaling regulates insect development, metamorphosis, reproduction and behavior [69, 70], JHAMT likely enhances its plasticity to modulate P. japonica life-history strategies. This JHAMT-mediated development plasticity may allow P. japonica to delay metamorphosis during resource limitation while promoting maturation under favorable conditions, thus optimizing fitness across heterogeneous environments.

Metabolic flexibility in fluctuating environments

Insects require sustained metabolic flexibility to fuel essential life processes and counteract environmental stressors. They typically obtain energy from lipids, carbohydrates and proteins to maintain energy homeostasis [71]. In insects, metabolic flexibility confers adaptive advantages in diverse environments, with potential implications for population dynamics, fundamental niches, and geographic ranges [72]. The expansion of metabolic gene families in P. japonica may enhance energy plasticity, allowing dynamic allocation by not only providing energy via lipid and carbohydrate metabolism for diapause, flight, and stress response [73, 74] but also supporting protein biosynthesis and immunomodulation through amino acid metabolism [75]. Together, these augmented metabolic pathways underpin a high degree of metabolic plasticity in P. japonica, facilitating the partitioning of resources among growth, reproduction, and stress resistance. This integrated metabolic adaptability constitutes a fundamental strategy for thriving under fluctuating ecological conditions.

In summary, this study provides initial insights into the divergence history and chromosomal evolution among different families of Coleoptera. Future research should prioritize investigations of the Coccinellidae family, specifically those targeting the chromosomal evolution of predatory ladybirds. Comparative genomic analysis revealed potential genetic information for the remarkable ecological adaptability of P. japonica, including key candidate genes such as OBPs, CYP450s, and histones. While these findings point to a possible crucial role for these genes in the adaptive evolution of this specie, further functional validation remains essential to confirm their specific contributions. For instance, one could employ RNAi to validate the role of CYP450s in detoxification and utilize CRISPR-Cas9 to decipher the functions of OBPs in host recognition and histones in developmental plasticity. Such investigations will not only deepen our understanding of the evolutionary mechanisms of Coccinellidae beetles but may also provide insights for biological pest control applications.

Conclusion

In this study, a comparative genomic analysis of P. japonica and related Coleoptera species was performed. Our phylogenetic analysis revealed the evolutionary history of Coccinellidae, dating the family’s origin to approximately 194.88 Mya and the divergence between P. japonica and H. axyridis to approximately 91.94 Mya. Genomic analysis further revealed a dynamic chromosomal evolution in P. japonica characterized by extensive fission and fusion events. Crucially, the genomic features identified in this study could serve as key drivers that underpin remarkable environmental adaptability. Chemosensory (OBPs) and water sensation gene families may enhance prey detection and osmoregulatory capacity, thereby optimizing predatory efficiency and survival. Detoxification-immune coadaptation potentially provides balanced defense against pesticides and pathogens, bolstering their agroecological fitness. Histone-mediated chromatin resilience and developmental stability may ensure genome integrity, developmental stability and flight performance under stress. Together with metabolic flexibility, these integrated adaptations likely optimize energy allocation between life-history strategies and stress resistance, further enhancing its niche adaptation. Collectively, our findings provide important insights into the main molecular mechanisms governing the ecological adaptation of P. japonica. In addition, this study offers theoretical insights into its persistent population dominance in agroecosystems while laying solid groundwork for future research on predator adaptation and biocontrol strategies.

Abbreviations

GO

Gene Ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

ABC

ATP-binding cassette transporter

JHAMT

Juvenile hormone acid O-methyltransferase

PSGs

Positive selected genes

OBP

Odorant-binding protein

MRP

Multidrug resistance protein

Authors’ contributions

Conceptualization, X.R.G. and L.J.Z.; experimental design, L.J.Z., and M.Z.; methodology and software, Y.S and S.F.J.; data curation, Y.M.L. and X.R.G.; investigation and data analysis, X.J.Y., Y.X., L.S.D. and Q.Z.; original draft preparation, X.J.Y.; review and editing, X.R.G. and L.J.Z. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (grant number: 32470470), and the Natural Science Foundation of Henan (grant number: 242300420157).

Data availability

All genomic data used for comparative analysis in this study were obtained from the NCBI database, except for *H. axyridis* (InsectBase database). The detailed BioProject accession numbers and download links of these 8 species are provided in Table 1.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.