Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application

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.

Selection of Sclerodermus pupariae Reference Genes for Quantitative Real-Time PCR

S. pupariae is a newly discovered species of parasitoid wasps. Research into its development, behavioral genetics, and molecular mechanisms provides valuable insights for improving integrated pest management strategies. Quantitative real-time PCR (qRT-PCR) is the most commonly used method for analyzing gene expression. This method requires the identification of stable reference genes to accurately evaluate transcriptional level variations. In this study, eight candidate reference genes (TUB, TBP, RPS18, GAPDH, 18S rRNA, RPL32, Actin, and EF1-α) were identified and evaluated for their suitability as reference genes. Gene expression levels across different developmental stages were analyzed using three software tools, GeNorm, NormFinder, and BestKeeper, and the online tool RefFinder. The overall ranking of reference gene stability was as follows: RPS18 > 18S rRNA > RPL32 > GAPDH > Actin > TUB > TPB > EF1-α. Ultimately, RPS18 was determined to be the most stable reference gene.

Extreme genetic signatures of local adaptation in a notorious rice pest, Chilo suppressalis

Climatic variation stands as a significant driving force behind genetic differentiation and the evolution of adaptive traits. Chilo (C.) suppressalis, commonly known as the rice stem borer, is a highly destructive pest that crucially harms rice production. The lack of natural population genomics data has hindered a more thorough understanding of its climate adaptation, particularly the genetic basis underlying adaptive traits. To overcome this obstacle, our study employed completely resequenced genomes of 384 individuals to explore the population structure, demographic history, and gene flow of C. suppressalis in China. This study observed that its gene flow occurred asymmetrically, moving from central populations to peripheral populations. Using genome-wide selection scans and genotype-environment association studies, we identified potential loci that may be associated with climatic adaptation. The most robust signal was found to be associated with cold tolerance, linked to a homeobox gene, goosecoid (GSC), whose expression level was significantly different in low and high latitudes. Moreover, downregulating the expression of this gene by RNAi enhances its cold tolerance phenotypes. Our findings have uncovered and delved into the genetic foundation of the ability of C. suppressalis to adapt to its environment. This is essential in ensuring the continued effectiveness and sustainability of novel control techniques.

Comparative genomic analyses reveal evidence for adaptive A-to-I RNA editing in insect Adar gene

Although A-to-I RNA editing leads to similar effects to A-to-G DNA mutation, nonsynonymous RNA editing (recoding) is believed to confer its adaptiveness by 'epigenetically' regulating proteomic diversity in a temporospatial manner, avoiding the pleiotropic effect of genomic mutations. Recent discoveries on the evolutionary trajectory of Ser>Gly auto-editing site in insect Adar gene demonstrated a selective advantage to having an editable codon compared to uneditable ones. However, apart from pure observations, quantitative approaches for justifying the adaptiveness of individual RNA editing sites are still lacking. We performed a comparative genomic analysis on 113 Diptera species, focusing on the Adar Ser>Gly auto-recoding site in Drosophila. We only found one species having a derived Gly at the corresponding site, and this occurrence was significantly lower than genome-wide random expectation. This suggests that the Adar Ser>Gly site is unlikely to be genomically replaced with G during evolution, and thus indicating the advantage of editable status over hardwired genomic alleles. Similar trends were observed for the conserved Ile>Met recoding in gene Syt1. In the light of evolution, we established a comparative genomic approach for quantitatively justifying the adaptiveness of individual editing sites. Priority should be given to such adaptive editing sites in future functional studies.

Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites

Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. In this study, we define a new category of RNA editing sites termed 'conserved editing with non-conserved recoding' and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. Our study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation.

Advances in aldo-keto reductases immobilization for biocatalytic synthesis of chiral alcohols

Chiral alcohols are essential building blocks of numerous pharmaceuticals and fine chemicals. Aldo-keto reductases (AKRs) constitute a superfamily of oxidoreductases that catalyze the reduction of aldehydes and ketones to their corresponding alcohols using NAD(P)H as a coenzyme. Knowledge about the crucial roles of AKRs immobilization in the biocatalytic synthesis of chiral alcohols is expanding. Herein, we reviewed the characteristics of various AKRs immobilization approaches, the applications of different immobilization materials, and the prospects of continuous flow bioreactor construction by employing these immobilized biocatalysts for synthesizing chiral alcohols. Finally, the opportunities and ongoing challenges for AKR immobilization are discussed and the outlook for this emerging area is analyzed.