Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles

Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory

BACKGROUND

Dietary shifts are major evolutionary steps that shape ecological niches and biodiversity. The beetle family Coccinellidae, commonly known as ladybirds, first transitioned from a fungivorous to an insectivorous and subsequently a plant diet. However, the molecular basis of this dietary diversification remained unexplored.

RESULTS

We investigated the molecular evolution of dietary shifts in ladybirds, focusing on the transitions from fungivory to carnivory (Coccinellidae) and from carnivory to herbivory (Epilachnini), by comparing 25 genomes and 62 transcriptomes of beetles. Our analysis shows that chemosensory gene families have undergone significant expansions at both nodes of diet change and were differentially expressed in feeding experiments, suggesting that they may be related to foraging. We found expansions of digestive and detoxifying gene families and losses of chitin-related digestive genes in the herbivorous ladybirds, and absence of most plant cell wall-degrading enzymes in the ladybirds dating from the transition to carnivory, likely indicating the effect of different digestion requirements on the gene repertoire. Immunity effector genes tend to emerge or have specific amino acid sequence compositions in carnivorous ladybirds and are downregulated under suboptimal dietary treatments, suggesting a potential function of these genes related to microbial symbionts in the sternorrhynchan prey.

CONCLUSIONS

Our study provides a comprehensive comparative genomic analysis to address evolution of chemosensory, digestive, detoxifying, and immune genes associated with dietary shifts in ladybirds. Ladybirds can be considered a ubiquitous example of dietary shifts in insects, and thus a promising model system for evolutionary and applied biology.

Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids

Metazoan parasites have played a major role in shaping innate immunity in animals. Insect hosts and parasitoid wasps are excellent models for illuminating how animal innate immune systems have evolved to neutralize these enemies. One such strategy relies on symbioses between insects and intracellular bacteria that express phage-encoded toxins. In some cases, the genes that encode these toxins have been horizontally transferred to the genomes of the insects. Here, we used genome editing in Drosophila melanogaster to recapitulate the evolution of two toxin genes-cytolethal distending toxin B (cdtB) and apoptosis inducing protein of 56kDa (aip56)-that were horizontally transferred likely from phages of endosymbiotic bacteria to insects millions of years ago. We found that a cdtB::aip56 fusion gene (fusionB), which is conserved in D. ananassae subgroup species, dramatically promoted fly survival and suppressed parasitoid wasp development when heterologously expressed in D. melanogaster immune tissues. We found that FusionB was a functional nuclease and was secreted into the host hemolymph where it targeted the parasitoid embryo's serosal tissue. Although the mechanism of toxicity remains unknown, when expressed ubiquitously, fusionB resulted in delayed development of late-stage fly larvae and eventually killed pupating flies. These results point to the salience of regulatory constraint in mitigating autoimmunity during the domestication process following horizontal transfer. Our findings demonstrate how horizontal gene transfer can instantly provide new, potent innate immune modules in animals.

Metabolic enhancement contributed by horizontal gene transfer is essential for dietary specialization in leaf beetles

Horizontal gene transfer (HGT) from bacteria to insects is widely reported and often associated with the adaptation and diversification of insects. However, compelling evidence demonstrating how HGT-conferred metabolic adjustments enable species to adapt to surrounding environment remains scarce. Dietary specialization is an important ecological strategy adopted by animals to reduce inter- and intraspecific competition for limited resources. Adults of the leaf beetle Plagiodera versicolora (Coleoptera) preferentially consume new leaves; nevertheless, we found that they selectively oviposit on mature leaves, thereby establishing a distinct dietary niche separation between adults and larvae. Based on the de novo assembled chromosome-level genome, we identified two horizontally transferred genes with cellulose degradation potential, belonging to the glycosyl hydrolase 48 family (GH48-1 and GH48-2). Prokaryotic expression of the HGTs confirmed the cellulose degradation capability of the two genes. Knockdown of GH48 significantly hampered the growth and survival rate of larvae feeding on mature leaves compared to wild-type larvae, with no similar effect observed in adults. Replenishing the GH48-expressing bacteria compensated for the knockdown of these two genes and recurred larval adaptability to mature leaves. Taken together, our results highlight the advantage and metabolic enhancement conferred by the two cellulose-degrading HGTs in P. versicolora larvae, enabling their development on cellulose-enriched mature leaves and underscoring the indispensable role of HGTs in facilitating the adaptation of leaf beetles to plants.

PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era

The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, prior to core analyses, traditional methods typically involve intricate and time-consuming procedures, including assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple sequence alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive data sets. In this study, we develop PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as a reference for phylogenetic and evolutionary analyses. Through testing with simulated data sets of species spanning the tree of life, PhyloAln demonstrates consistently robust performance compared with other reference-based tools across different data types, sequencing technologies, coverages, and species, with percent completeness and identity at least 50 percentage points higher in the alignments. Additionally, we validate the efficacy of PhyloAln in removing a minimum of 90% foreign and 70% cross-contamination issues, which are prevalent in sequencing data but often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments (completeness mostly larger than 80%, identity larger than 90%) and reconstructing robust phylogenies using real data sets of transcriptomes of ladybird beetles, plastid genes of peppers, or ultraconserved elements of turtles. With these advantages, PhyloAln is expected to facilitate phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.

Chromosome-level genome assembly of the giant ladybug Megalocaria dilatata

The giant ladybug Megalocaria dilatata (Fabricius) is a potential biocontrol agent and a valuable model for coccinellid genomics and evolutionary biology. However, the lack of a reference genome for M. dilatata has impeded further explorations into its evolution and constrained its use in pest management. Here, we assembled and annotated a high-quality, chromosome-level genome of M. dilatata. The resulting assembly spans 772.3 Mb, with a scaffold N50 of 72.48 Mb and a GC content of 34.23%. The Hi-C data aided in anchoring the assembly onto 10 chromosomes ranging from 43.35 to 108.16 Mb. We identified 493.33 Mb of repeat sequences, accounting for 63.88% of the assembled genome. Our gene prediction identified 25,346 genes, with 81.89% annotated in public protein databases. The genome data will provide a valuable resource for studying the biology and evolution of Coccinellidae, aiding in pest control strategies and advancing research in the field.

The genome sequence of the orange ladybird, Halyzia sedecimguttata (Linnaeus, 1758)

We present a genome assembly from an individual Halyzia sedecimguttata (the orange ladybird, Arthropoda; Insecta; Coleoptera, Coccinellidae). The genome sequence is 919.1 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 27,547 protein coding genes.

A chromosome-level genome assembly of the Henosepilachna vigintioctomaculata provides insights into the evolution of ladybird beetles

The ladybird beetle Henosepilachna vigintioctomaculata is an economically significant oligophagous pest that induces damage to many Solanaceae crops. An increasing number of studies have examined the population and phenotype diversity of ladybird beetles. However, few comparative genome analyses of ladybird beetle species have been conducted. Here, we obtained a high-quality chromosome-level genome assembly of H. vigintioctomaculata using various sequencing technologies, and the chromosome-level genome assembly was ~581.63 Mb, with 11 chromosomes successfully assembled. The phylogenetic analysis showed that H. vigintioctomaculata is a more ancient lineage than the other three sequenced ladybird beetles, Harmonia axyridis, Propylea japonica, and Coccinella septempunctata. We also compared positively selected genes (PSGs), transposable elements (TEs) ratios and insertion times, and key gene families associated with environmental adaptation among these ladybird beetles. The pattern of TEs evolution of H. vigintioctomaculata differs from the other three ladybird beetles. The PSGs were associated with ladybird beetles development. However, the key gene families associated with environmental adaptation in ladybird beetles varied. Overall, the high-quality draft genome sequence of H. vigintioctomaculata provides a useful resource for studies of beetle biology, especially for the invasive biology of ladybird beetles.

Exploring new genomic territories with emerging model insects

Improvements in reference genome generation for insects and across the tree of life are extending the concept and utility of model organisms beyond traditional laboratory-tractable supermodels. Species or groups of species with comprehensive genome resources can be developed into model systems for studying a large variety of biological phenomena. Advances in sequencing and assembly technologies are supporting these emerging genome-enabled model systems by producing resources that are increasingly accurate and complete. Nevertheless, quality controls including assessing gene content completeness are required to ensure that these data can be included in expanding catalogues of high-quality references that will greatly advance understanding of insect biology and evolution.

Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892)

BACKGROUND

Members of the genus Novius Mulsant, 1846 (= Rodolia Mulsant, 1850) (Coleoptera, Coccinellidae), play important roles in the biological control of cotton cushion scale pests, especially those belonging to Icerya. Since the best-known species, the vedalia beetle Novius cardinalis (Mulsant, 1850) was introduced into California from Australia, more than a century of successful use in classical biological control, some species of Novius have begun to exhibit some field adaptations to novel but related prey species. Despite their economic importance, relatively little is known about the underlying genetic adaptations associated with their feeding habits. Knowledge of the genome sequence of Novius is a major step towards further understanding its biology and potential applications in pest control.

RESULTS

We report the first high-quality genome sequence for Novius pumilus (Weise, 1892), a representative specialist of Novius. Computational Analysis of gene Family Evolution (CAFE) analysis showed that several orthogroups encoding chemosensors, digestive, and immunity-related enzymes were significantly expanded (P < 0.05) in N. pumilus compared to the published genomes of other four ladybirds. Furthermore, some of these orthogroups were under significant positive selection pressure (P < 0.05). Notably, transcriptome profiling demonstrated that many genes among the significantly expanded and positively selected orthogroups, as well as genes related to detoxification were differentially expressed, when N. pumilus feeding on the nature prey Icerya compared with the no feeding set. We speculate that these genes are vital in the Icerya adaptation of Novius species.

CONCLUSIONS

We report the first Novius genome thus far. In addition, we provide comprehensive transcriptomic resources for N. pumilus. The results from this study may be helpful for understanding the association of the evolution of genes related to chemosensing, digestion, detoxification and immunity with the prey adaptation of insect predators. This will provide a reference for future research and utilization of Novius in biological control programs. Moreover, understanding the possible molecular mechanisms of prey adaptation also inform mass rearing of N. pumilus and other Novius, which may benefit pest control.

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes

A growing body of evidence has underscored the role of horizontal gene transfer (HGT) in animal evolution. Previously, we discovered the horizontal transfer of the gene encoding the eukaryotic genotoxin cytolethal distending toxin B (cdtB) from the pea aphid Acyrthosiphon pisum secondary endosymbiont (APSE) phages to drosophilid and aphid nuclear genomes. Here, we report cdtB in the nuclear genome of the gall-forming "swede midge" Contarinia nasturtii (Diptera: Cecidomyiidae) via HGT. We searched all available gall midge genome sequences for evidence of APSE-to-insect HGT events and found five toxin genes (aip56, cdtB, lysozyme, rhs, and sltxB) transferred horizontally to cecidomyiid nuclear genomes. Surprisingly, phylogenetic analyses of HGT candidates indicated APSE phages were often not the ancestral donor lineage of the toxin gene to cecidomyiids. We used a phylogenetic signal statistic to test a transfer-by-proximity hypothesis for animal HGT, which suggested that microbe-to-insect HGT was more likely between taxa that share environments than those from different environments. Many of the toxins we found in midge genomes target eukaryotic cells, and catalytic residues important for toxin function are conserved in insect copies. This class of horizontally transferred, eukaryotic cell-targeting genes is potentially important in insect adaptation.

Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri

BACKGROUND

The ladybird beetle Cryptolaemus montrouzieri Mulsant, 1853 (Coleoptera, Coccinellidae) is used worldwide as a biological control agent. It is a predator of various mealybug pests, but it also feeds on alternative prey and can be reared on artificial diets. Relatively little is known about the underlying genetic adaptations of its feeding habits.

RESULTS

We report the first high-quality genome sequence for C. montrouzieri. We found that the gene families encoding chemosensors and digestive and detoxifying enzymes among others were significantly expanded or contracted in C. montrouzieri in comparison to published genomes of other beetles. Comparisons of diet-specific larval development, survival and transcriptome profiling demonstrated that differentially expressed genes on unnatural diets as compared to natural prey were enriched in pathways of nutrient metabolism, indicating that the lower performance on the tested diets was caused by nutritional deficiencies. Remarkably, the C. montrouzieri genome also showed a significant expansion in an immune effector gene family. Some of the immune effector genes were dramatically downregulated when larvae were fed unnatural diets.

CONCLUSION

We suggest that the evolution of genes related to chemosensing, digestion, and detoxification but also immunity might be associated with diet adaptation of an insect predator. These findings help explain why this predatory ladybird has become a successful biological control agent and will enable the optimization of its mass rearing and use in biological control programs.