Chromosome-level genome assembly of cotton thrips Thrips tabaci (Thysanoptera: Thripidae).

Cotton thrip, Thrips tabaci is a major polyphagous pest widely distributed on a variety of crops around the world, causing huge economic losses to agricultural production. Due to its biological and genomic characteristics, this pest can reproduce quickly and develop resistance to various pesticides in a very short time. However, the lack of high-quality reference genomes has hindered deeper gene function exploration and slows down the development of new management strategies. Here, we assembled a high-quality genome of T. tabaci at the chromosome level for the first time by using Illumina, PacBio long reads, and Hi-C technologies. The 329.59 Mb genome was obtained from 320 contigs, with a contig N50 of 1.53 Mb, and 94.21% of the assembly was anchored to 18 chromosomes. In total, 17,816 protein-coding genes were annotated, and 96.78% of BUSCO genes were fully represented. In conclusion, this high-quality genome provides a valuable genetic basis for our understanding of the biology of T. tabaci and contributes to the development of management strategies for cotton thrip.

A chromosome-level genome assembly of the legume pod borer, Maruca vitrata Fabricius (Lepidoptera: Crambidae).

Maruca vitrata, a significant pest of legumes, impacts food security in Asia and Africa. This study presents a high-quality genome assembly of M. vitrata, utilizing advanced sequencing technologies including Nanopore long-read, MGI short-read, and Hi-C. The genome, totaling 482.3 Mb with a contig N50 of 2.91 Mb, features 41.58% repetitive sequences and encompasses 13,320 protein-coding genes. We performed comparative genomic analyses to affirm the accuracy and completeness of the protein sequences assembled, ensuring the assembly's integrity. Additionally, the annotation of 83 Cytochrome P450 (CYP) genes further confirms the comprehensive nature of the genome assembly and its annotations. This genome assembly not only deepens our understanding of M. vitrata biology but also supports the development of sustainable pest management strategies. This research highlights the importance of genomics in advancing sustainable agricultural solutions through innovative pest management approaches.

Phylogeny and evolution of hemipteran insects based on expanded genomic and transcriptomic data.

BACKGROUND: Hemiptera is the fifth species-rich order of insects and the most species-rich order of hemimetabolous insects, including numerous insect species that are of agricultural or medical significance. Despite much effort and recent advance in inferring the Hemiptera phylogeny, some high-level relationships among superfamilies remain controversial. RESULTS: We sequenced the genomes of 64 hemipteran species from 15 superfamilies and the transcriptomes of two additional scale insect species, integrating them with existing genomic and transcriptomic data to conduct a comprehensive phylogenetic analysis of Hemiptera. Our datasets comprise an average of 1625 nuclear loci of 315 species across 27 superfamilies of Hemiptera. Our analyses supported Cicadoidea and Cercopoidea as sister groups, with Membracoidea typically positioned as the sister to Cicadoidea + Cercopoidea. In most analyses, Aleyrodoidea was recovered as the sister group of all other Sternorrhyncha. A sister-group relationship was supported between Coccoidea and Aphidoidea + Phylloxeroidea. These relationships were further supported by four-cluster likelihood mapping analyses across diverse datasets. Our ancestral state reconstruction indicates phytophagy as the primary feeding strategy for Hemiptera as a whole. However, predation likely represents an ancestral state for Heteroptera, with several phytophagous lineages having evolved from predatory ancestors. Certain lineages, like Lygaeoidea, have undergone a reversal transition from phytophagy to predation. Our divergence time estimation placed the diversification of hemipterans to be between 60 and 150 million years ago. CONCLUSIONS: By expanding phylogenomic taxon sampling, we clarified the superfamily relationships within the infraorder Cicadomorpha. Our phylogenetic analyses supported the sister-group relationship between the superfamilies Cicadoidea and Cercopoidea, and the superfamily Membracoidea as the sister to Cicadoidea + Cercopoidea. Our divergence time estimation supported the close association of hemipteran diversification with the evolutionary success and adaptive radiation of angiosperms during the Cretaceous period.

Chromosome-level genome assembly of the planthopper Nilaparvata muiri.

The Nilaparvata muiri (Hemiptera: Delphacidae) is a sibling species of a destructive rice insect pest, the brown planthopper (BPH), Nilaparvata lugens. Here, we generated a high-quality chromosome-level genome assembly of N. muiri using a combination of the PacBio HiFi sequencing, Illumina short-read sequencing and Hi-C scaffolding technologies. The genome assembly (524.9 Mb) is anchored to 15 pseudochromosomes, with a scaffold N50 of 43.3 Mb and 99.1% BUSCO completeness. It contains 188.1 Mb repeat sequences and 13204 protein-coding genes. As a closely related species within the same genus as the significant pest, N. lugens, the chromosome-level genome assembly of N. muiri will provide important support for the better analysis of pathogenicity mechanisms of N. lugens based on comparative genomics.

Chromosome-level genome assembly of Chinese water Scorpion Ranatra chinensis (Heteroptera: Nepidae).

Heteroptera (the true bugs), one of the most diverse lineages of insects, diversified in feeding strategies and living habitats, and thus become an ideal lineage for studies on adaptive evolution. Chinese water scorpion Ranatra chinensis (Heteroptera: Nepidae) is a predaceous bug living in lentic water systems, representing an ideal model for studying habitat transition and adaptation to water environment. However, genetic studies on this water bug remain limited. Here, we obtained a chromosome-level genome of R. chinensis using PacBio HiFi long reads and Hi-C sequencing reads. The total assembly size of genome is 867.89 Mb, with a scaffold N50 length of 26.48 Mb and the GC content of 39.50%. All contigs were assembled into 23 pseudo-chromosomes (N = 19 A + X1X2X3X4), and we predicted 18,424 protein-coding genes in this genome. This study will provide valuable genomic resources for future studies on the biology, water adaptation, and genome evolution of water bugs.

Population genomic evidence of a putative 'far-west' African cryptic taxon in the Anopheles gambiae complex.

The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identified a putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather may have originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, this taxon lacks insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.

Genome-wide analysis reveals transcriptional and translational changes during diapause of the Asian corn borer (Ostrinia furnacalis).

BACKGROUND: Diapause, a pivotal phase in the insect life cycle, enables survival during harsh environmental conditions. Unraveling the gene expression profiles of the diapause process helps uncover the molecular mechanisms that underlying diapause, which is crucial for understanding physiological adaptations. In this study, we utilize RNA-seq and Ribo-seq data to examine differentially expressed genes (DEGs) and translational efficiency during diapause of Asian corn borer (Ostrinia furnacalis, ACB). RESULTS: Our results unveil genes classified as "forwarded", "exclusive", "intensified", or "buffered" during diapause, shedding light on their transcription and translation regulation patterns. Furthermore, we explore the landscape of lncRNAs (long non-coding RNAs) during diapause and identify differentially expressed lncRNAs, suggesting their roles in diapause regulation. Comparative analysis of different types of diapause in insects uncovers shared and unique KEGG pathways. While shared pathways highlight energy balance, exclusive pathways in the ACB larvae indicate insect-specific adaptations related to nutrient utilization and stress response. Interestingly, our study also reveals dynamic changes in the HSP70 gene family and proteasome pathway during diapause. Manipulating HSP protein levels and proteasome pathway by HSP activator or inhibitor and proteasome inhibitor affects diapause, indicating their vital role in the process. CONCLUSIONS: In summary, these findings enhance our knowledge of how insects navigate challenging conditions through intricate molecular mechanisms.

Chromosome-level genome assembly of the forest pest Achelura yunnanensis (Lepidoptera: Zygaenidae).

Achelura yunnanensis is a destructive pest of forests, causing substantial damage on tree growth and severe economic losses. Additionally, as a daytime-active moth, this species also holds important scientific value for investigating the genetic mechanisms governing day-night activity patterns of Lepidoptera. To facilitate effective pest control and deepen our understanding of the diurnal behavior's genetic basis of moths, genomic data for this species are crucial. In this study, we present a chromosome-level reference genome of A. yunnanensis (368.15 Mb in 32 chromosomes; scaffold N50 = 12.61 Mb; BUSCO completeness = 98.0%). Genome annotation shows that the new assembly comprises 37.10% (136.55 Mb) repetitive elements, 1,828 non-coding RNAs, and 15,523 protein-coding genes. Genes involved in lipid metabolism and xenobiotics biodegradation and metabolism, such as cytochrome P450 families, experienced significant expansion in the A. yunnanensis genome. The chromosome-level genome of A. yunnanensis provides a valuable genomic resource for devising novel pest control strategies, and will also help to study the genetic mechanism of the shift of diurnal behavior in Lepidoptera.

Chromosome-level genome assembly of the morabine grasshopper Vandiemenella viatica19.

Morabine grasshoppers in the Vandiemenella viatica species group, which show karyotype diversity, have been studied for their ecological distribution and speciation in relation to their genetic and chromosomal diversity. They are good models for studying sex chromosome evolution as "old" and newly emerged sex chromosomes co-exist within the group. Here we present a reference genome for the viatica19 chromosomal race, that possesses the ancestral karyotype within the group. Using PacBio HiFi and Hi-C sequencing, we generated a chromosome-level assembly of 4.09 Gb in span, scaffold N50 of 429 Mb, and complete BUSCO score of 98.1%, containing 10 pseudo-chromosomes. We provide Illumina datasets of males and females, used to identify the X chromosome. The assembly contains 19,034 predicted protein-coding genes, and a total of 75.21% of repetitive DNA sequences. By leveraging HiFi reads, we mapped the genome-wide distribution of methylated bases (5mC and 6 mA). This comprehensive assembly offers a robust reference for morabine grasshoppers and supports further research into speciation and sex chromosome diversification within the group and its related species.

Genomic diversity and population structure of Carniolan honey bee in its native habitat.

BACKGROUND: Research into the genetic diversity of honey bee (Apis mellifera L.) populations has become increasingly significant in recent decades, primarily due to population declines attributed to human activities and climate change. As a species of great importance, breeding programs that leverage understanding of genomic diversity could offer solutions to mitigate these challenges. The objective of this study was to examine the genomic diversity and population structure of Carniolan honey bees (Apis mellifera carnica) using the Illumina SNP chip on a large honey bee sample collected from Central and South-Eastern European countries. The study also aims to offer recommendations for future breeding programs. RESULTS: Our analysis involved Discriminant Analysis of Principal Components (DAPC), heterozygosity, admixture analysis, fixation indices (FST), Neighbour-Joining tree, gene flow and Isolation-by-distance analysis. DAPC indicated distinct separation between the Carniolan and Italian honey bee (Apis mellifera ligustica) populations, whereas the admixture analysis revealed varying levels of gene flow and genetic admixture within the Carniolan honey bee populations, demonstrating closer relationships between specific geographic regions (confirmed by Isolation-by-distance analysis). Furthermore, the research of heterozygosity, genomic inbreeding, pairwise FST values, and Neighbour-Joining tree provided insights into the patterns of genetic differentiation and similarity among the populations of Carniolan honey bee within its natural habitat. We have observed genetic homogeneity of the Carniolan honey bee population when considered in a broader genetic/geographical context. However, the Carniolan honey bee has sufficient genetic diversity in its geographical home range that needs to be carefully monitored and maintained. CONCLUSIONS: This study provides important insights into the genetic composition, differentiation, and relationships among Carniolan honey bee populations in Central and South-Eastern European countries. The findings are crucial for conservation efforts, breeding programs, and sustainable beekeeping practices. They emphasise the importance of considering genetic factors and population structure in the breeding and management of honey bees. By understanding these genetic relationships, we can develop strategies to preserve genetic diversity, improve breeding outcomes, and ensure the resilience of honey bee populations in the face of environmental changes and challenges. This knowledge can also inform policy makers and stakeholders on best practices to maintain healthy bee populations, which are vital for ecosystem services and agricultural productivity.

An expanded odorant-binding protein mediates host cue detection in the parasitic wasp Baryscapus dioryctriae basis of the chromosome-level genome assembly analysis.

BACKGROUND: Baryscapus dioryctriae (Chalcidodea: Eulophidae) is a parasitic wasp that parasitizes the pupae of many Pyralidae members and has been used as a biological control agent against Dioryctria pests of pinecones. RESULTS: This B. dioryctriae assembly has a genome size of 485.5 Mb with a contig N50 of 2.17 Mb, and scaffolds were assembled onto six chromosomes using Hi-C analysis, significantly increasing the scaffold N50 to 91.17 Mb, with more than 96.13% of the assembled bases located on chromosomes, and an analysis revealed that 94.73% of the BUSCO gene set. A total of 54.82% (279.27 Mb) of the assembly was composed of repetitive sequences and 24,778 protein-coding genes were identified. Comparative genomic analysis demonstrated that the chemosensory perception, genetic material synthesis, and immune response pathways were primarily enriched in the expanded genes. Moreover, the functional characteristics of an odorant-binding protein (BdioOBP45) with ovipositor-biased expression identified from the expanded olfactory gene families were investigated by the fluorescence competitive binding and RNAi assays, revealing that BdioOBP45 primarily binds to the D. abietella-induced volatile compounds, suggesting that this expanded OBP is likely involved in locating female wasp hosts and highlighting a direction for future research. CONCLUSIONS: Taken together, this work not only provides new genomic sequences for the Hymenoptera systematics, but also the high-quality chromosome-level genome of B. dioryctriae offers a valuable foundation for studying the molecular, evolutionary, and parasitic processes of parasitic wasps.

Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila.

A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila, a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across Drosophila mojavensis, Drosophila arizonae, and Drosophila navojoa. We use these data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa.

Chromosome-level genome assembly of predatory Arma chinensis.

Arma chinensis is a natural enemy that preys on various species and can suppress agricultural and forest pests in the orders Lepidoptera and Coleoptera. Here, we aimed to determine the genome of A. chinensis assembled at the chromosome-level using PacBio and Hi-C technologies. The assembled genome was 986 Mb, with a contig N50 of 2.40 Mb, scaffold N50 of 134.98 Mb, and BUSCO completeness of 96.10%. Hi-C data aided in anchoring the assembly onto seven chromosomes. A sequence of ~ 496.2 Mb was annotated as a repeat element, constituting 51.15% of the genome. We functionally annotated 84.79% of 20,853 predicted protein-encoding genes. This high-quality A. chinensis genome provides a novel genomic resource for future research on Pentatomidae insects.

Chromosome-level genome assembly of Oriental chestnut gall wasp (Dryocosmus kuriphilus).

Dryocosmus kuriphilus, commonly known as the chestnut gall wasp, belongs to the family Cynipidae and is native to China. It is a highly invasive insect species causing serious damage to chestnut trees and has rapidly spread to various continents, including Europe, North America, and Oceania. The D. kuriphilus has become one of the important pests of chestnut plants in the world and is listed as a quarantine object by the European and Mediterranean Plant Protection Organization (EPPO). In this study, we used PacBio long reads, Illumina short reads, and Hi-C sequencing data to construct a chromosome-level assembly of the D. kuriphilus genome. The assembled genome includes 14,729 contigs with a total length of 2.28 Gb and a contig N50 of 0.8 Mb. With Hi-C technology, 2.17 Gb (95.02%) of contigs were anchored and oriented into the 10 pseudochromosomes with the scaffold N50 of 198.8 Mb and the scaffold N90 of 158.8 Mb. In total, 24,086 protein-coding genes were predicted in the assembled D. kuriphilus genome as the reference gene set. A total of 1.82 Gb repeats (occupying 79.7% of the genome), including 1.42 Gb of transposable elements and 0.40 Gb of tandem repeats, were identified in D. kuriphilus genome. In the evaluation of completeness, the BUSCO analysis determined a level of 98.1% completeness for the assembled genome sequences based on the Insecta database (OrthoDB version 10). The high-quality genome assembly of D. kuriphilus will not only provide a valuable reference for the study of its evolutionary history and genetic structure but also facilitate the research of host-pest interactions and invasiveness. Moreover, this genome assembly will promote in the development of effective management strategies to mitigate the economic and ecological impacts of this invasive pest on chestnut trees and ecosystems.

Genomic data provide insights into the classification of extant termites.

The higher classification of termites requires substantial revision as the Neoisoptera, the most diverse termite lineage, comprise many paraphyletic and polyphyletic higher taxa. Here, we produce an updated termite classification using genomic-scale analyses. We reconstruct phylogenies under diverse substitution models with ultraconserved elements analyzed as concatenated matrices or within the multi-species coalescence framework. Our classification is further supported by analyses controlling for rogue loci and taxa, and topological tests. We show that the Neoisoptera are composed of seven family-level monophyletic lineages, including the Heterotermitidae Froggatt, Psammotermitidae Holmgren, and Termitogetonidae Holmgren, raised from subfamilial rank. The species-rich Termitidae are composed of 18 subfamily-level monophyletic lineages, including the new subfamilies Crepititermitinae, Cylindrotermitinae, Forficulitermitinae, Neocapritermitinae, Protohamitermitinae, and Promirotermitinae; and the revived Amitermitinae Kemner, Microcerotermitinae Holmgren, and Mirocapritermitinae Kemner. Building an updated taxonomic classification on the foundation of unambiguously supported monophyletic lineages makes it highly resilient to potential destabilization caused by the future availability of novel phylogenetic markers and methods. The taxonomic stability is further guaranteed by the modularity of the new termite classification, designed to accommodate as-yet undescribed species with uncertain affinities to the herein delimited monophyletic lineages in the form of new families or subfamilies.

Genome-wide identification and molecular evolution of elongation family of very long chain fatty acids proteins in Cyrtotrachelus buqueti.

To reveal the molecular function of elongation family of very long chain fatty acids(ELO) protein in Cyrtotrachelus buqueti, we have identified 15 ELO proteins from C.buqueti genome. 15 CbuELO proteins were located on four chromosomes. Their isoelectric points ranged from 9.22 to 9.68, and they were alkaline. These CbuELO proteins were stable and hydrophobic. CbuELO proteins had transmembrane movement, and had multiple phosphorylation sites. The secondary structure of CbuELO proteins was mainly α-helix. A total of 10 conserved motifs were identified in CbuELO protein family. Phylogenetic analysis showed that molecular evolutionary relationships of ELO protein family between C. buqueti and Tribolium castaneum was the closest. Developmental transcriptome analysis indicated that CbuELO10, CbuELO13 and CbuELO02 genes were key enzyme genes that determine the synthesis of very long chain fatty acids in pupae and eggs, CbuELO6 and CbuELO7 were that in the male, and CbuELO8 and CbuELO11 were that in the larva. Transcriptome analysis under different temperature conditions indicated that CbuELO1, CbuELO5, CbuELO12 and CbuELO14 participated in regulating temperature stress responses. Transcriptome analysis at different feeding times showed CbuELO12 gene expression level in all feeding time periods was significant downregulation. The qRT-PCR experiment verified expression level changes of CbuELO gene family under different temperature and feeding time conditions. Protein-protein interaction analysis showed that 9 CbuELO proteins were related to each other, CbuELO1, CbuELO4 and CbuELO12 had more than one interaction relationship. These results lay a theoretical foundation for further studying its molecular function during growth and development of C. buqueti.

Chromosome-level genome assembly of the invasive pest Pseudococcus jackbeardsleyi (Hemiptera: Pseudococcidae).

Among over 2,000 species of mealybugs (Hemiptera: Pseudococcidae), only 13 genomes have been published so far, seriously limiting the researches on the phylogeny and adaptive evolution of this group. The continuous publication of mealybug genomes will significantly facilitate our exploration of the biological characteristics, detrimental attributes, and control strategies of the Pseudococcidae family. Jack Beardsley mealybug (Pseudococcus jackbeardsleyi) as one of the hazardous invasive pests, it could cause enormous losses to the fruit and vegetable industries worldwide. Herein, we combined Nanopore long-read, short-read Illumina and Hi-C sequencing, generating a high-quality chromosome-level genome assembly of P. jackbeardsleyi. The genome size was determined to be 334.818 Mb, which was assembled into 5 linkage groups with a N50 of 67.233 Mb. The BUSCO analysis demonstrated the completeness of the genome assembly and annotation are 95.7% and 92.8%, respectively. The developed high-quality genome will serve as an asset for delving into the genetic mechanisms underlying the invasiveness of P. jackbeardsleyi, thereby offering a crucial theoretical foundation for the prevention and management of Pseudococcidae pests.

Insect cuticular protein; gene expression, genomic structure, transcriptional regulation, speculated cuticular structure, clarified through the genomic analysis of Bombyx mori.

JH and ecdysone signaling regulate insect metamorphosis through the master transcription factors, Krüppel homolog 1 (kr-h1), Broad-Complex (BR-C), and E93. Ecdysone signaling activates successively expressed ecdysone responsive transcription factors (ERTFs), and the interaction between ERTFs determines the expression profiles of ERTFs themselves. Through the construction of expressed sequence tag (EST) database of Bombyx mori from many tissues, the existence of a large number of cuticular protein (CP) genes was identified in wing disc cDNA library of the 3 days after the start of wandering (W3). From the genomic analysis, 12 types of CP clusters of CP genes were identified. DNA sequences of CP genes revealed the duplication of CP genes, which suggests to reflect the insect evolution. These CP genes responded to ecdysone and ecdysone pulse; therefore, CP genes were applied for the analysis of transcriptional regulation by ERTF. The binding sites of ERTF have been reported to exist upstream of CP genes in several insects, and the activation of CP genes occurred by the binding of ERTFs. Through the analysis, the following were speculated; the successive appearance of ERTFs and the activation of target genes resulted in the successively produced CPs and cuticular layer. The sequence of the ERTF and CP gene expression was the same at larval to pupal and pupal to adult transformation. The involvement of several ERTFs in one CP gene expression was also clarified; BmorCPG12 belongs to group showing expression peak at W3 and was regulated by two ERTFs; BHR3 and ßFTZ-F1, BmorCPH2 belongs to group showing expression peak at P0 and was regulated by two ERTFs; ßFTZ-F1 and E74A. The involvement of BHR39 as a negative regulator of CP gene expression was found. Larval, pupal, and adult cuticular layers were supposed to be constructed by the combination of different and similar types of CPs, through the expressed timing of CP genes.

A chromosomal-level genome assembly of Serrognathus titanus Boisduval, 1835 (Coleoptera: Lucanidae).

The Stag beetle (Coleoptera: Lucanidae) is a fascinating group, often considered one of the most primitive within the Scarabaeoidea. They are valuable models for studying beetle evolution. However, the lack of high-quality genomes hinders our understanding of the evolution and ecology of Lucanidae. In this study, we present a chromosome-level genome of Serrognathus titanus by combining PacBio HiFi long reads, Illumina short reads, and Hi-C data. The genome spans 384.07 Mb, with a scaffold N50 size of 75.81 Mb, and most contigs (97.45%, 374.30 Mb) were anchored into six chromosomes. Our BUSCO analysis of the assembly indicates a completeness of 97.6% (n = 1,367), with 92.8% single-copy BUSCOs and 4.8% duplicated BUSCOs identified. Additionally, we found that the genome contains 43.87% (168.50 Mb) repeat elements and identified 14,263 predicted protein-coding genes. The high-quality genome of S. titanus provides valuable genomic information for comprehending the evolution and ecology of Lucanidae.

Chromosomal-level genome assembly of Hylurgus ligniperda: insights into host adaptation and environmental tolerance.

BACKGROUND: Hylurgus ligniperda (Coleoptera: Curculionidae) is a worldwide forest quarantine pest. It is widely distributed, has many host tree species, and possesses strong adaptability. To explore its environmental adaptability and the related molecular mechanisms, we conducted chromosome-level genome sequencing and analyzed the transcriptome under different environmental factors, identifying key expressed genes. RESULTS: We employed PacBio, Illumina, and Hi-C sequencing techniques to assemble a 520 Mb chromosomal-level genome of H. ligniperda, obtaining an N50 of 39.97 Mb across 138 scaffolds. A total of 10,765 protein-coding genes were annotated after repeat masking. Fourteen chromosomes were identified, among which Hyli14 was determined to be the sex chromosome. Survival statistics were tested over various growth periods under high temperature and low humidity conditions. The maximum survival period of adults reached 292 days at 25 °C, 65% relative humidity. In comparison, the maximum survival period was 14 days under 35 °C, 65% relative humidity, and 106 days under 25°C, 40% relative humidity. This indicated that environmental stress conditions significantly reduced adults' survival period. We further conducted transcriptome analysis to screen for potentially influential differentially expressed genes, such as CYP450 and Histone. Subsequently, we performed gene family analysis to gain insights into their functions and interactions, such as CYP450 and Histone. CYP450 genes affected the detoxification metabolism of enzymes in the Cytochrome P450 pathway to adapt to different environments. Histone genes are involved in insect hormone biosynthesis and longevity-regulating pathways in H. ligniperda to adapt to environmental stress. CONCLUSIONS: The genome at the chromosome level of H. ligniperda was assembled for the first time. The mortality of H. ligniperda increased significantly at 35 ℃, 65% RH, and 25 ℃, 40% RH. CYP450 and Histone genes played an important role in response to environmental stress. This genome offers a substantial genetic resource for investigating the molecular mechanisms behind beetle invasion and spread.