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

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.

Effect of Ephestia kuehniella Eggs on Development and Transcriptome of the Ladybird Beetle Propylea japonica

The eggs of the Mediterranean flour moth, Ephestia kuehniella, are frequently utilized as alternative diets and have demonstrated promising outcomes when consumed by various insects. Nonetheless, the specific reasons for their effectiveness remain unclear. In our study, we assessed the developmental performance of the ladybird Propylea japonica when fed E. kuehniella eggs, alongside 12 factitious prey or artificial diets. Our findings revealed that ladybirds fed E. kuehniella eggs displayed a performance comparable to those fed the natural prey Megoura crassicauda. Transcriptome profiling of larvae raised on E. kuehniella eggs and M. crassicauda revealed that genes upregulated in the former group were enriched in metabolic pathways associated with carbohydrates, lipids, and other essential nutrients. This suggests that E. kuehniella eggs may have a higher nutrient content compared to natural prey. Furthermore, a notable downregulation in the expression of immune effector genes, such as Attacin and Coleoptericin, was observed, which might be attributed to the lower microbial content in E. kuehniella eggs compared to M. crassicauda. We suggest that the difference between E. kuehniella eggs and M. crassicauda as food sources for P. japonica lies in their nutrient and microbial contents. These findings provide valuable insights for the advancement of innovative artificial breeding systems for natural enemies.

Differential Proteomics Analysis Unraveled Mechanisms of Arma chinensis Responding to Improved Artificial Diet

Simple Summary

Arma chinensis Fallou is a predaceous stink bug that can effectively control many kinds of agricultural and forest pests, such as fall armyworm, cotton bollworm and Colorado potato beetle. An insect-free artificial diet comprising chicken egg, tuna fish and raw pig liver was developed for A. chinensis. Several biological characteristics were diminished for A. chinensis reared on the artificial diet compared to the pupae of Chinese oak silk moth. Changes in the formulation of the diet were made in response to the transcriptome results and tested using biological characteristics. Several parameters were improved over 6 generations, although the improved artificial diet remained inferior to the pupae of Chinese oak silk moth regarding egg viability, fecundity, body weight, and nymphal development time. The current study reported the differential proteomic analysis revealing the mechanism of A. chinensis responding to the improved artificial diet. This information will be used to optimize the formulation of the artificial diet and decrease the cost of mass rearing in A. chinensis.

Abstract

The development of artificial diets could considerably simplify and reduce the cost of mass rearing of natural enemies compared to conventional rearing methods. However, improvement of artificial diets can be tedious, convoluted and often uncertain. For accelerating diet development, a better method that can offer informative feedback to target deficiencies in diet improvement is required. Our previous research demonstrated several biological characteristics were diminished in the insect predator, Arma chinensis Fallou, fed on an artificial diet formulated with the aid of transcriptomic methods compared to the Chinese oak silk moth pupae. The present study reports differential proteomic analysis by iTRAQ-PRM, which unravels the molecular mechanism of A. chinensis responding to improvements in the artificial diet. Our study provides multivariate proteomic data and provides comprehensive sequence information in studying A. chinensis. Further, the physiological roles of the differentially expressed proteins and pathways enable us to explain several biological differences between natural prey-fed and improved diet-fed A. chinensis, and subsequent proposed reformulation optimizations to artificial diets.

Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)

BACKGROUND

The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings.

FINDINGS

We present a high-quality reference genome of P. flavescens, which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution.

CONCLUSIONS

The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control.

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.