Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure

Genomics of insect natural enemies in agroecosystems

Currently, a wealth of genomic data are now accessible for numerous insect natural enemies, serving as valuable resources that deepen our understanding of the genetic basis of biocontrol traits in these organisms. We summarize the current state of genome sequencing and highlight candidate genes related to biocontrol traits that hold promise for genetic improvement. We also review the recent population genomic studies in biological control and the discovery of potential insecticidal genes in parasitoid wasps. Collectively, current genomic works have shown the powerful ability to identify candidate genes responsible for desirable traits or promising effectors. However, further functional study is necessary to gain a mechanistic understanding of these genes, and future efforts are also needed to develop suitable approaches to translate genomic insights into field applications.

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.

Using ecological niches to determine potential habitat suitability for Psacothea hilaris (Coleoptera: Cerambycidae) and its natural enemies in China under future climates

Climate change impacts the distribution of pests and its natural enemies, prompting this study to investigate the dynamics and shifts in distribution under current and future climate conditions. The spatial pattern of Psacothea hilaris (Pascoe) (Coleoptera: Cerambycidae) in China was analyzed, and the MaxEnt model was optimized to predict the potential geographic distribution of P. hilaris and its two natural enemies (Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) and Dendrocopos major (Linnaeus) (Piciformes: Picidae)) in China, to further analyze the key environmental factors affecting the survival of P. hilaris and its natural enemies, and to determine the potential of using D. helophoroides and D. major as natural enemies to control P. hilaris. The results showed that the suitable ranges of P. hilaris and natural enemies are expanding under the influence of climate change, and both have migrated to higher latitudes. The potential ranges of D. helophoroides, D. major, and P. hilaris are highly similar. It is noteworthy that the potential range of D. helophoroides completely covers the potential range of P. hilaris. This indicates that D. helophoroides and D. major can be employed as biological control agents to manage P. hilaris populations. This study provides a theoretical framework and empirical evidence for the development of early warning and green control strategies for P. hilaris.

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.

CncC-Keap1-P450s pathway is involved in the detoxification of emamectin benzoate in the spongy moth Lymantria dispar

The detoxification of insecticides in insects is dependent on the expression and activity of multiple detoxification enzymes. As an important modulator of detoxification enzymes, the CncC-Keap1 pathway was involved in the detoxification of various pesticides. However, whether the CncC-Keap1 pathway is involved in the detoxification of emamectin benzoate (EMB) is unclear. In this study, we cloned the LdCncC and LdKeap1 from spongy moths (Lymantria dispar). Our results showed that EMB exposure induced oxidative stress, and activated the CncC-Keap1 pathway at mRNA and protein levels. Removing ROS by N-acetylcysteine remarkably decreased H2O2 levels and restored the expression of LdCncC and LdKeap1. The silencing LdCncC, not LdKeap1, by dsRNA significantly decreased the cytochrome P450 activities, and increased the sensitivity of larvae to EMB. Besides, the expression of CYP6B7v1, CYP321A7 and CYP4S4v1 were significantly decreased after silencing LdCncC. Notably, the knockdown of CYP6B7v1, CYP321A7 or CYP4S4v1 significantly increased the mortality induced by EMB exposure. Therefore, we proposed that activation of CncC-Keap1 pathway induced by ROS increased the detoxification of EMB in spongy moths by regulating the expression of CYP6B7v1, CYP321A7 and CYP4S4v1. Our study strengthened the understanding of the detoxification of EMB from the perspective of CncC-Keap1-P450s pathway.

Integrated behavior and transcriptomic analysis provide valuable insights into the response mechanisms of Dastarcus helophoroides Fairmaire to light exposure

Light traps have been widely used to monitor and manage pest populations, but natural enemies are also influenced. The Dastarcus helophoroides Fairmaire is an important species of natural enemy for longhorn beetles. However, the molecular mechanism of D. helophoroides in response to light exposure is still scarce. Here, integrated behavioral, comparative transcriptome and weighted gene co-expression network analyses were applied to investigate gene expression profiles in the head of D. helophoroides at different light exposure time. The results showed that the phototactic response rates of adults were 1.67%-22.5% and females and males displayed a negative phototaxis under different light exposure [6.31 × 1018 (photos/m2/s)]; the trapping rates of female and male were influenced significantly by light exposure time, diel rhythm, and light wavelength in the behavioral data. Furthermore, transcriptome data showed that a total of 1,052 significantly differentially expressed genes (DEGs) were identified under different light exposure times relative to dark adaptation. Bioinformatics analyses revealed that the "ECM-receptor interaction," "focal adhesion," "PI3K-Akt signaling," and "lysosome" pathways were significantly downregulated with increasing light exposure time. Furthermore, nine DEGs were identified as hub genes using WGCNA analysis. The results revealed molecular mechanism in negative phototactic behavior response of D. helophoroides under the light exposure with relative high intensity, and provided valuable insights into the underlying molecular response mechanism of nocturnal beetles to light stress.