Genome-wide identification of cuticle protein superfamily in Frankliniella occidentalis provide insight into the control of both insect vectors and plant virus.

The structural cuticle proteins (CPs) play important roles in the development and fitness of insects. However, knowledge about CP gene superfamily is limited in virus-transmitting insect vectors, although its importance on transmission of plant virus has been gradually emphasized. In this study, the genome-wide identification of CP superfamily was conducted in western flower thrips Frankliniella occidentalis that is the globally invasive pest and plant virus vector pest. The pest transmits notorious tomato spotted wilt virus (TSWV) around the world, causing large damage to a wide array of plants. One hundred and twenty-eight F. occidentalis CP genes (FoCPs) were annotated in this study and they were classified into 10 distinct families, including 68 CPRs, 16 CPAP1s, 6 CPAP3s, 2 CPCFCs, 10 Tweedles, 4 CPFs, 16 CPLCPs, and 6 CPGs. The comprehensive analysis was performed including phylogenetic relationship, gene location and gene expression profiles during different development stages of F. occidentalis. Transcriptome analysis revealed more than 30% FoCPs were upregulated at least 1.5-fold when F. occidentalis was infected by TSWV, indicating their potential involvement in TSWV interactions. Our study provided an overview of F. occidentalis CP superfamily. The study gave a better understand of CP's role in development and virus transmission, which provided clues for reducing viral damages through silencing CP genes in insect vectors.

Inbreeding effects on different lineages of Thrips tabaci (Thysanoptera: Thripidae).

Inbreeding can have detrimental effects on reproductive fitness, but the extent of lineage-specific variation in these effects remains poorly understood. This study investigated the effects of brother and sister inbreeding on reproductive fitness in 2 lineages (L1 and T) of T. tabaci. Inbred females from both lineages exhibited a significant reduction in longevity compared with the control group. The L1 lineage experienced a 27% and 43% decrease in longevity in the F2 and F3 generations, respectively, while the T lineage showed a similar trend with a 30% and 44% decrease. The T lineage consistently displayed slightly longer lifespans than the L1 lineage across all generations. Brother and sister inbreeding also led to a decrease in fecundity rates in both lineages. In the F3 generation, the number of eggs laid decreased by 59% compared with the F2 generation. The T lineage consistently exhibited slightly lower fecundity rates compared with the L1 lineage. Egg hatchability rates declined with subsequent inbreeding, with the F3 generation showing lower rates compared with the F2 generation. However, the T lineage did not exhibit a significant difference in inbreeding depression for egg hatchability rates, while the L1 lineage demonstrated a noticeable decrease. Deformities observed in male L1 lineage resulting from inbreeding were consistent with disruptions in normal developmental processes, affecting various body parts such as legs, antennae, and wings. Continued inbreeding increased susceptibility to inbreeding depression in terms of longevity, fecundity, and egg hatchability.

A chromosome-level genome for the flower thrips Frankliniella intonsa.

The flower thrips Frankliniella intonsa (Thysanoptera: Thripidae) is a common insect found in flowers of many plants. Sometimes, F. intonsa causes damage to crops through direct feeding and transmission of plant viruses. Here, we assembled a chromosomal level genome of F. intonsa using the Illumina, Oxford Nanopore (ONT), and Hi-C technologies. The assembled genome had a size of 209.09 Mb, with a contig N50 of 997 bp, scaffold N50 of 13.415 Mb, and BUSCO completeness of 92.5%. The assembled contigs were anchored on 15 chromosomes. A set of 14,109 protein-coding genes were annotated in the genome with a BUSCO completeness of 95.0%. The genome contained 491 non-coding RNA and 0.57% of interspersed repeats. This high-quality genome provides a valuable resource for understanding the ecology, genetics, and evolution of F. intonsa, as well as for controlling thrips pests.

Emerging challenges in the management of Orthotospoviruses in Indian agriculture.

Orthotospoviruses, a genera of negative-sense ssRNA viruses transmitted by thrips, have gained significant attention in recent years due to their detrimental impact on diverse crops, causing substantial economic losses and posing threats to food security. Orthotospoviruses are characterised by a wide range of symptoms in plants, including chlorotic/necrotic spots, vein banding, and fruit deformation. Seven species, including four definite and three tentative species in the genus Orthotospovirus, have so far been documented on the crops of the Indian subcontinent. Management of Orthotospoviruses under field conditions is challenging since they have a wide host range, adaptation to versatile environmental conditions, a lack of promising resistance sources, and the ubiquitous nature of thrips and their transmission through a propagative manner. Our present review elucidates the significance, molecular biology and evolutionary relationship of Orthotospoviruses; vector population; and possible management strategies for Orthotospoviruses and their vectors in the scenario of the Indian subcontinent.

The extraordinary rearrangement of mitochondrial genome of the wheat pest, Aptinothrips stylifer and the mitochondrial phylogeny of Thripidae (Thysanoptera).

The mitochondrial gene order in Thysanoptera is notably distinct and highly rearranged, with each species exhibiting its own unique arrangement. To elucidate the relationship between gene rearrangements and phylogeny, the complete mitochondrial genome (mitogenome) of the wheat pest, Aptinothrips stylifer, was sequenced and assembled, spanning a total length of 16,033 bp. Compared with the ancestral arthropod mitogenome, significant rearrangement differences were evident in A. stylifer, whereas the gene order between A. stylifer and Anaphothrips obscurus was similar. Phylogenetic trees were reconstructed based on all 13 protein-coding gene sequences using Bayesian inference and maximum-likelihood methods, both yielding similar topological structures. Notably, A. stylifer was robustly clustered with A. obscurus, affirming its classification within Anaphothrips genus group. This exemplifies the potential correlation between gene rearrangements and phylogeny in the Thripidae family. Additionally, the mitogenome of A. stylifer exhibited several atypical features, including: (1) Three putative control regions (CRs) in close proximity, with CR2 and CR3 displaying partial similarity, and CR1 differing in base composition; (2) Two transfer RNAs (tRNAs), trnS1 and trnV, lacking the DHU arm; (3) Two ribosomal RNA (rRNA) genes inverted and positioned distant from each other; (4) Negative AT and GC skew (AT skew = -0.001, GC skew = -0.077); (5) One transposition (nad6), one inverse transposition (trnQ), four inversions (trnF, trnH, trnC, and gene block nad1-trnL1-rrnL-trnV-rrnS), and four tandem duplication random loss events; and (6) Two protein-coding genes, nad2 and atp8, terminated with an incomplete stop codon "T".

Uridine diphosphate glucosyltransferases are involved in spinosad resistance in western flower thrips Frankliniella occidentalis (Pergande).

Uridine diphosphate glucosyltransferases (UGTs) play crucial roles in the insect detoxification system and are associated with pesticide resistance. Our previous transcriptomic analysis of spinosad-susceptible (Ivf03) and resistant (NIL-R) Frankliniella occidentalis revealed numerous upregulated UGT genes in the NIL-R strain, suggesting their potential contribution to spinosad resistance. To investigate this hypothesis, here we conducted UGT activity assays and spinosad induction experiments, employing RNA interference (RNAi) techniques for gene function validation. We found significantly elevated UGT activity in the NIL-R strain compared to Ivf03, with 5-nitrouracil showing a substantial synergistic effect on the resistant strain. Eighteen UGT genes were identified in F. occidentalis, with gene expansion and duplication observed within families UGT466, 467, and 468. Ten out of the eighteen UGTs exhibited higher expression levels in NIL-R, specifically FoUGT466B1, FoUGT468A3, and FoUGT468A4 consistently being upregulated across nymphs, males, and females. RNAi-based functional validation targeting these three UGT genes led to increased susceptibility to spinosad in a life stage-, sex-, and dose-dependent manner. These results indicate that UGTs are indeed involved in spinosad resistance in F. occidentalis, and the effects are dependent on life stage, sex, and dose. Therefore, sustainable control for F. occidentalis resistance should always consider these differential responses.

A new species of the genus Scirtothrips (Thysanoptera, Thripidae) from India.

A new species of Scirtothrips is described from India, S. donumdei, collected on leaves of Senegalia pennata (Fabaceae). Partial mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene sequence of the species was sequenced and the annotated sequence was submitted to NCBI GenBank.

Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta).

The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age-related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple-CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.

Chromosome-level genome assembly of the flower thrips Frankliniella intonsa.

As an economically important insect pest, the flower thrips Frankliniella intonsa (Trybom) causes great damage to host plants by directly feeding and indirectly transmitting various pathogenic viruses. The lack of a well-assembled genomic resource has hindered our understanding of the genetic basis and evolution of F. intonsa. In this study, we used Oxford Nanopore Technology (ONT) long reads and High-through chromosome conformation capture (Hi-C) linked reads to construct a high-quality reference genome assembly of F. intonsa, with a total size of 225.5 Mb and a contig N50 of 3.37 Mb. By performing the Hi-C analysis, we anchored 91.68% of the contigs into 15 pseudochromosomes. Genomic annotation uncovered 17,581 protein-coding genes and identified 20.09% of the sequences as repeat elements. BUSCO analysis estimated over 98% of genome completeness. Our study is at the first time to report the chromosome-scale genome for the species of the genus Frankliniella. It provides a valuable genomic resource for further biological research and pest management of the thrips.

Invasive flower thrips, Thrips parvispinus (Karny) occurrence, host expansion and genetic diversification in a tropical poly-crop ecosystem.

BACKGROUND: Invasive black flower thrips Thrips parvispinus (Karny) has recently emerged as a significant threat to Indian chilli production. Identifying T. parvispinus became difficult due to the complex presence of thrips species in Indian chilli and allied ecosystems. Pest management success depends on assessing invasive pests genetic populations and their distribution in newly habituated areas. METHODS AND RESULTS: The current study investigated the genetic diversity and phylogeographic structure of T. parvispinus across major chilli-growing zones representing different agro-climatic conditions in Tamil Nadu. The species-specific chaetotaxy characteristics of T. parvispinus and molecular analysis of the mtCOI gene were used to confirm that the species T. parvispinus has expanded rapidly in three regions (North Western, Western and Cauvery delta), sparsely in one (Southern) and absent from two (hilly and high rainfall). Fifteen allied crops in chilli/capsicum growing tracts served as host plants for T. parvispinus. A shrub species, namely Littleleaf boxwood, Buxus microphylla Siebold & Zucc., is described as a host plant for the first time. On capsicum and chilli, T. parvispinus and Scirtothrips dorsalis coexisted. Thrips palmi, T. tabaci, Frankliniella schultzei, and Microcephalothrips abdominalis co-occurring alongside T. parvispinus on allied crops. CONCLUSION: Molecular characterization and haplotype identification help define the genetic composition of T. parvispinus and serve as a foundation for efficient monitoring and creation of Integrated Pest Management (IPM) strategies. As a result, the genetic data presented in this work strongly argues that T. parvispinus as a population is resolving itself towards a fixed state through natural selection that spans its native range globally along with low genetic diversity [Hd: 0.771].

Relaxed purifying selection pressure drives accelerated and dynamic gene rearrangements in thrips (Insecta: Thysanoptera) mitochondrial genomes.

Insect mitochondrial genomes (mitogenome) generally present a typical gene order, which is considered as the ancestral arrangement. All sequenced mitogenomes in the Thysanoptera display high levels of gene rearrangement. Due to limited number of thrips mitogenomes sequenced, how gene rearrangement may be shaped by evolution remain unclear. Here, we analyzed 33 thrips mitogenomes, including 14 newly sequenced. These mitogenomes were diverse in organization, nucleotides substitution and gene arrangements. We found 28 highly rearranged gene orders with the breakpoints of gene rearrangements from 25 to 33. Reconstruction of the ancestors mitochondrial gene arrangements states indicated that Tubulifera have more complex pathways than Terebrantia in the gene order evolution. Molecular calibration estimated that divergence of two suborders occurred in the middle Triassic while the radiation of thrips was associated with the arose and flourish of angiosperm. Our evolutionary hypothesis testing suggests that relaxation of selection pressure enabled the early phase of Thysanoptera evolution, followed by a stronger selective pressure fixed diversification. Our analyses found gene inversion increases the nonsynonymous substitution rates and provide an evolutionary hypothesis driving the diverse gene orders.

Extant thrips diverged in the early tertiary period.

Thysanoptera, commonly known as thrips, are diverse tiny insects whose earliest fossil record dates back to the Triassic period. Since there are few studies on the divergence time of taxa under Thysanoptera, this study used 13 mitochondrial coding protein genes to reconstruct the phylogenetic tree with divergence time of 26 species of this order and show a reliable phylogenetic relationship of thrips species. The time tree of this study shows that most extant thrips diverged in the early Tertiary period, while the fossil records also support that most extinct thrips appeared in this period. This study expands our understanding of the evolution of thrips and provides a feasible way of using multiple mitochondrial genes to establish robust phylogenetic relationships and explore divergence time between species.

Tiny insects, big troubles: a review of BOLD's COI database for Thysanoptera (Insecta).

DNA Barcoding is an important tool for disciplines such as taxonomy, phylogenetics and phylogeography, with Barcode of Life Data System (BOLD) being the largest database of partial cytochrome c oxidase subunit I (COI) sequences. We provide the first extensive revision of the information available in this database for the insect order Thysanoptera, to assess: how many COI sequences are available; how representative these sequences are for the order; and the current potential of BOLD as a reference library for specimen identification and species delimitation. The COI database at BOLD currently represents only about 5% of the over 6400 valid thrips species, with a heavy bias towards a few species of economic importance. Clear Barcode gaps were observed for 24 out of 33 genera evaluated, but many outliers were also observed. We suggest that the COI sequences available in BOLD as a reference would not allow for accurate identifications in about 30% of Thysanoptera species in this database, which rises to 40% of taxa within Thripidae, the most sampled family within the order. Thus, we call for caution and a critical evaluation in using BOLD as a reference library for thrips Barcodes, and future efforts should focus on improving the data quality of this database.

Genetic diversity of thrips populations on Allium species around the world.

Thrips are a serious pest in many crops. In onion cultivation, Thrips tabaci is the most important, but not the only thrips species causing damage. We investigated which thrips species affects onion and related species worldwide, how much genetic variation there is within T. tabaci populations, and how this evolves. Furthermore, we determined the reproductive mode and the correlation between the genetic and geographic distances. Thrips samples from infested onions or related species were obtained from 14 different locations worldwide. Species and haplotypes were determined through DNA barcoding with the mitochondrial Cytochrome Oxidase subunit I (COI) gene. Thrips tabaci was the most commonly observed species, but Scirtothrips dorsalis, Thrips palmi, Frankliniella intonsa, Frankliniella occidentalis and Frankliniella tenuicornis were also found, especially at the beginning of the growing seasons and depending on the location. The Nei's genetic distance within T. tabaci was less than 5% and the haplotypes were clustered into two phylogenetic groups, each linked to a specific mode of reproduction, thelytokous or arrhenotokous. Thelytokous thrips were more common and more widely distributed than arrhenotokous thrips. A high percentage of heteroplasmy was detected in the arrhenotokous group. Heteroplasmic thrips were only found in populations where thelytokous and arrhenotokous were present in sympatry. Some T. tabaci haplotypes were present in high frequency at several sampled locations. No correlation was found between the genetic and geographic distances, which points to anthropic activities spreading thrips haplotypes throughout the world.

A chromosome-level genome assembly of Stenchaetothrips biformis and comparative genomic analysis highlights distinct host adaptations among thrips.

Insects have a limited host range due to genomic adaptation. Thysanoptera, commonly known as thrips, occupies distinct feeding habitats, but there is a lack of comparative genomic analyses and limited genomic resources available. In this study, the chromosome-level genome of Stenchaetothrips biformis, an oligophagous pest of rice, is assembled using multiple sequencing technologies, including PacBio, Illumina short-reads, and Hi-C technology. A 338.86 Mb genome is obtained, consisting of 1269 contigs with a contig N50 size of 381 kb and a scaffold N50 size of 18.21 Mb. Thereafter, 17,167 protein-coding genes and 36.25% repetitive elements are annotated. Comparative genomic analyses with two other polyphagous thrips, revealing contracted chemosensory-related and expanded stress response and detoxification gene families in S. biformis, potentially facilitating rice adaptation. In the polyphagous thrips species Frankliniella occidentalis and Thrips palmi, expanded gene families are enriched in metabolism of aromatic and anthocyanin-containing compounds, immunity against viruses, and detoxification enzymes. These expansion gene families play crucial roles not only in adapting to hosts but also in development of pesticide resistance, as evidenced by transcriptome results after insecticides treatment. This study provides a chromosome-level genome assembly and lays the foundation for further studies on thrips evolution and pest management.

The Chromosome-Level Genome Assembly of Bean Blossom Thrips (Megalurothrips usitatus) Reveals an Expansion of Protein Digestion-Related Genes in Adaption to High-Protein Host Plants.

Megalurothrips usitatus (Bagnall) is a destructive pest of legumes, such as cowpea. The biology, population dynamics and control strategies of this pest have been well studied. However, the lack of a high-quality reference genome for M. usitatus has hindered the understanding of key biological questions, such as the mechanism of adaptation to feed preferentially on high-protein host plants and the resistance to proteinase inhibitors (PIs). In this study, we generated a high-resolution chromosome-level reference genome assembly (247.82 Mb, 16 chromosomes) of M. usitatus by combining Oxford Nanopore Technologies (ONT) and Hi-C sequencing. The genome assembly showed higher proportions of GC and repeat content compared to other Thripinae species. Genome annotation revealed 18,624 protein-coding genes, including 4613 paralogs that were preferentially located in TE-rich regions. GO and KEGG enrichment analyses of the paralogs revealed significant enrichment in digestion-related genes. Genome-wide identification uncovered 506 putative digestion-related enzymes; of those, proteases, especially their subgroup serine proteases (SPs), are significantly enriched in paralogs. We hypothesized that the diversity and expansion of the digestion-related genes, especially SPs, could be driven by mobile elements (TEs), which promote the adaptive evolution of M. usitatus to high-protein host plants with high serine protease inhibitors (SPIs). The current study provides a valuable genomic resource for understanding the genetic variation among different pest species adapting to different plant hosts.

The Sw-5b NLR Immune Receptor Induces Early Transcriptional Changes in Response to Thrips and Mechanical Modes of Inoculation of Tomato spotted wilt orthotospovirus.

The NLR (nucleotide-binding leucine-rich repeat) class immune receptor Sw-5b confers resistance to Tomato spotted wilt orthotospovirus (TSWV). Although Sw-5b is known to activate immunity upon recognition of the TSWV movement protein NSm, we know very little about the downstream events that lead to resistance. Here, we investigated the Sw-5b-mediated early transcriptomic changes that occur in response to mechanical and thrips-mediated inoculation of TSWV, using near-isogenic tomato lines CNPH-LAM 147 (Sw5b+/+) and Santa Clara (Sw-5b-/-). We observed earlier Sw-5b-mediated transcriptional changes in response to thrips-mediated inoculation compared with that in response to mechanical inoculation of TSWV. With thrips-mediated inoculation, differentially expressed genes (DEGs) were observed at 12, 24, and 72 h postinoculation (hpi). Whereas with mechanical inoculation, DEGs were observed only at 72 hpi. Although some DEGs were shared between the two methods of inoculation, many DEGs were specific to either thrips-mediated or mechanical inoculation of TSWV. In response to thrips-mediated inoculation, an NLR immune receptor, cysteine-rich receptor-like kinase, G-type lectin S-receptor-like kinases, the ethylene response factor 1, and the calmodulin-binding protein 60 were induced. Fatty acid desaturase 2-9, cell death genes, DCL2b, RIPK/PBL14-like, ERF017, and WRKY75 were differentially expressed in response to mechanical inoculation. Our findings reveal Sw-5b responses specific to the method of TSWV inoculation. Although TSWV is transmitted in nature primarily by the thrips, Sw-5b responses to thrips inoculation have not been previously studied. Therefore, the DEGs we have identified in response to thrips-mediated inoculation provide a new foundation for understanding the mechanistic roles of these genes in the Sw-5b-mediated resistance. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Sublethal effects of emamectin benzoate on development, reproduction, and vitellogenin and vitellogenin receptor gene expression in Thrips hawaiiensis (Thysanoptera: Thripidae).

Thrips hawaiiensis (Morgan) (Thysanoptera: Thripidae) is a sap-sucking pest that seriously damages several crops and reduces their economic value. Exposure to low concentrations of insecticides may have a sublethal effect on surviving insects. In order to provide a reference for the rational application of emamectin benzoate, its sublethal effects on the development and reproduction of T. hawaiiensis were evaluated. Pupal development time was significantly shorter in T. hawaiiensis treated with sublethal concentrations of emamectin benzoate (LC10 and LC20) than in control. Female adult longevity and female total longevity were significantly longer following LC20 treatment than in the control and LC10 treatment groups. Nevertheless, male adult longevity and male total longevity were significantly shorter in the LC10 treatment group than in the control and LC20 treatment groups. The sublethal concentration of emamectin benzoate (LC20) significantly shortened the preadult stages and the mean generation. Meanwhile, it significantly increased the finite rate of increase, intrinsic rate of increase, and net reproductive rate. The fecundity was significantly higher after LC20 treatment than after LC10 and control treatments. Compared with the control group, the LC10 and LC20 groups of T. hawaiiensis adults showed a significantly higher expression of the vitellogenin (Vg) and vitellogenin receptor (VgR) genes, which played a key role in increasing their fecundity. These findings suggest that short-term exposure to sublethal concentrations of emamectin benzoate may lead to a resurgence and secondary outbreak of T. hawaiiensis infestation. The results have practical applications for the management of this important and noxious pest.

Double sodium channel mutation, I265T/L1014F, is possibly related to pyrethroid-resistant in Thrips palmi.

Thrips palmi Karny (Thysanoptera: Thripidae) can harm a variety of agricultural crops and transmit plant viruses, causing heavy economic losses. In the Hainan province of China, pyrethroids were sprayed widely to control T. palmi, which leaded to resistance to pyrethroids in T. palmi. The bioassay has shown that the resistance ratio of T. palmi to pyrethroids increases annually. Resistance ratio to λ-cyhalothrin has increased from 10.711 to 23.321 and to cypermethrin has increased from 5.507 to 23.051 for 3 years, 2020-2022. The double mutation (I265T/L1014F) was identified from the field strain for the first time, which were located in the domains I and II of the voltage-gated sodium channel of T. palmi, respectively. The double mutation is probably the reason for the higher resistance of T. palmi in Hainan. The frequencies of the double mutation were 53.33% in HN2020, 70.00% in HN2021, and 96.67% in HN2022. Results indicated that T. palmi had developed different degrees of resistance to pyrethroids in Hainan. This study provides theoretical guidance for the use of insecticides in the field control of thrips.

Chromosome-level genome assembly of bean flower thrips Megalurothrips usitatus (Thysanoptera: Thripidae).

Bean flower thrips Megalurothrips usitatus is a staple pest of cowpea and other legumes and causes dramatic economic losses. Its small size allows for easy concealment, and large reproductive capacity easily leads to infestations. Despite the importance of a genome in developing novel management strategies, genetic studies on M. usitatus remain limited. Thus, we generated a chromosome-level M. usitatus genome using a combination of PacBio long read and Hi-C technologies. The assembled genome was 238.14 Mb with a scaffold N50 of 13.85 Mb. The final genome was anchored into 16 pseudo-chromosomes containing 14,000 genes, of which 91.74% were functionally annotated. Comparative genomic analyses revealed that expanded gene families were enriched in fatty acid metabolism and detoxification metabolism (ABC transporters), and contracted gene families were strongly associated with chitin-based cuticle development and sensory perception of taste. In conclusion, this high-quality genome provides an invaluable resource for us to understand the thrips' ecology and genetics, contributing to pest management.