Abstract Background The plant bug, Pachypeltis micranthus Mu et Liu (Hemiptera: Miridae), is an effective potential biological control agent for Mikania micrantha H.B.K. (Asteraceae; one of the most notorious invasive weeds worldwide). However, limited knowledge about this species hindered its practical application and research. Accordingly, sequencing the genome of this mirid bug holds great significance in controlling M. micrantha. Results Here, 712.72 Mb high-quality chromosome-level scaffolds of P. micranthus were generated, of which 707.51 Mb (99.27%) of assembled sequences were anchored onto 15 chromosome-level scaffolds with contig N50 of 16.84 Mb. The P. micranthus genome had the highest GC content (42.43%) and the second highest proportion of repetitive sequences (375.82 Mb, 52.73%) than the three other mirid bugs (i.e., Apolygus lucorum, Cyrtorhinus lividipennis, and Nesidiocoris tenuis). Phylogenetic analysis showed that P. micranthus clustered with other mirid bugs and diverged from the common ancestor approximately 200 million years ago. Gene family expansion and/or contraction were analyzed, and significantly expanded gene families associated with P. micranthus feeding and adaptation to M. micrantha were manually identified. Compared with the whole body, transcriptome analysis of the salivary gland revealed that most of the upregulated genes were significantly associated with metabolism pathways and peptidase activity, particularly among cysteine peptidase, serine peptidase, and polygalacturonase; this could be one of the reasons for precisely and highly efficient feeding by the oligophagous bug P. micranthus on M. micrantha. Conclusion Collectively, this work provides a crucial chromosome-level scaffolds resource to study the evolutionary adaptation between mirid bug and their host. It is also helpful in searching for novel environment-friendly biological strategies to control M. micrantha. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-023-09445-8. Keywords: Pachypeltis micranthus, Chromosome-level scaffolds, Mikania micrantha, Genome assembly, Adaptation, Salivary gland transcriptome Background The plant bug, Pachypeltis micranthus Mu et Liu (Hemiptera: Miridae) (Fig. [35]1a_I-VIII), was first discovered in Yunnan, China, in 2008 and identified as a novel species in 2017 [[36]1, [37]2]. The bug feeds gregariously on the leaves of Mikania micrantha H.B.K. (Asteraceae; the top 100 of the world’s worst invasive plants). Feeding by P. micranthus leads to leaf discolouration (Fig. [38]1a_IX), delays stem growth, sharply reduces the number of flowers in M. micrantha, and may lead to death in established plants [[39]2, [40]3]. Furthermore, field and laboratory experiments have further demonstrated that, compared to other closely related plants, companion plants, economically important crops, and horticulture and landscape plants, P. micranthus specifically oviposits on M. micrantha and poses a threat to M. micrantha. The bug also relies on M. micrantha to complete its life cycle [[41]4, [42]5]. Hence, P. micranthus can be an efficient biological agent to control M. micrantha. Fig. 1. [43]Fig. 1 [44]Open in a new tab Biology and genome characteristics of Pachypeltis micranthus. a Life cycle of the plant bug P. micranthus (I-VIII) and the damage symptom to Mikania micrantha (IX). (I) Eggs, (II-VI) first to fifth instar nymph, (VII) male adult bug, (VIII) female adult bug, (IX) and damage from nymphs and adult bug feeding. b Genomic landscape of P. micranthus. From the outer to inner circles: (I) sizes of fifteen chromosome-level scaffolds, the scale bar indicates the length of the chromosome-level scaffold in Mb; (II) density of transposable elements (TEs); (III) density of tandem repeats (TRs); (IV) gene density; (V) GC density; (VI) Collinearity within the genome of P. micranthus. Densities are calculated in 100 Kb windows. c The Hi-C chromosomal interaction map for the fifteen chromosome-level scaffolds of P. micranthus. d Chromosomes of gonadal cells of P. micranthus in mitotic metaphase (2n = 30, 1000 X). e Different stages of sperm in P. micranthus. Red arrows indicate the sperms, and the numbers (I—V) next to the red arrows represent the partial process of sperm formation. f Chromosome-level scaffolds synteny based on CDS pairwise alignment between P. micranthus, Apolygus lucorum, and Cyrtorhinus lividipennis. Coloured lines indicate shared syntenic blocks An adequate understanding of the mechanism of P. micranthus feeding on M. micrantha is beneficial for the availability of this bug in M. micrantha control. P. micranthus is an oligophagous insect that feeds on the leaves of M. micrantha and small amounts of leaves from Eupatorium odoratum, Ageratina adenophora (Sprengel) R. King and H. Robinson, and Gynura crepidioides Benth [[45]4]. Insects can recognize their plant hosts based on chemical signals emitted by the plants with the chemosensory systems [i.e., odorant-binding proteins (OBPs), chemosensory proteins (CSPs), and odorant receptors (ORs)] [[46]6, [47]7]. The chemosensory system plays a crucial role not only in the processes of locating food but also shelter, mates, and oviposition [[48]8, [49]9]. Therefore, many studies have reported extensive chemosensory genes in other mirid bugs (Apolygus lucorum, Cyrtorhinus lividipennis, Lygus lineolaris, and Lygus hesperus) [[50]10, [51]11]. Myrcene was already confirmed as one of the most abundant volatiles in M. micrantha and showed a potent attractive effect on this bug [[52]12]. So far, however, only nine OBPs, three CSPs, and one OR gene have been reported in P. micranthus [[53]13], which is insufficient to study the attraction mechanism of M. micrantha to this bug. In most insects, salivary glands are important labial glands that secrete saliva, an essential chemical substance with biological activities and complex composition, including many digestive enzymes (e.g., proteinases, phospholipase, esterase, serine proteases, trehalase) [[54]14–[55]16]. Like other mirid bugs, P. micranthus feed by inserting its stylet into plant tissues and injecting enzyme-containing saliva (digestive enzymes); the injected saliva is responsible for stylet lubrication and preliminary digestion of plant tissues [[56]14, [57]17, [58]18]. The salivary enzymes remaining in the feeding site cause continuous tissue damage for an extended period, leading to a decrease in the growth rate and loss of flowers [[59]19–[60]21]. The primary damage caused by mirid bugs during feeding is due to saliva rather than mechanical damage caused by stylet [[61]20]. Moreover, the component in saliva also has a detoxification effect and acts as an effector to induce or inhibit plant defence responses [[62]22]. Therefore, mirid bugs feeding can trigger severe damage to plants, such as leaf discolouration, necrosis of the feeding site, organ abscission, flower bud abortion, and even the death of the entire plant [[63]23, [64]24]. Based on these symptoms, P. micranthus can control M. micrantha, but harmful agricultural mirid bugs can cause crop yield reduction [[65]2, [66]17]. In the past, salivary gland transcriptome analysis has mainly focused on blood feeding [[67]18]. For mirid bugs, only the salivary gland transcriptomes of Lygus lineolaris were reported [[68]18, [69]21], providing valuable information for omnivorous mirid bugs. However, the salivary gland transcriptome of P. micranthus is needed, and generating this data will increase our knowledge of how the oligophagous mirid bugs can adapt to the specific host. Plants can produce many specialized chemical substances that resist the herbivores’ challenges. Herbivory can seriously reduce the survival rate and fecundity of local plants. In crops, invading herbivorous insects will lead to severe yield loss [[70]25, [71]26]. Herbivore-induced plant defence is divided into direct defences, such as toxins or anti-digestive proteins, and indirect defences, such as the plant volatiles that attract the natural enemies of herbivores [[72]27]. Continued exposure to toxic or anti-digestive compounds is a defence option for herbivores to adapt to host plants, often making better-defended plants the targets of herbivores. The process of this co-evolution leads to the host plant specialization of insects. Thus, most herbivores feed on only a few host plants [[73]26]. Insects rely primarily on four detoxification enzyme families, including cytochrome P450s (P450s), glutathione S-transferases (GSTs), carboxylesterases (CCEs), and ATP-binding cassette transporters (ABCs), to metabolize the toxic substances from the food and environment [[74]28, [75]29]. Liu et al. reported the A. lucorum genome and many detoxification enzymes of glutathione GSTs and P450s, explaining a better detoxification system of toxins and adaptation to the environment in A. lucorum [[76]11]. There are numerous bioactive secondary metabolites in M. micrantha tissues [[77]30]. Notably, although the extracts from M. micrantha show insect avoidance, toxicity, and antibacterial activity [[78]31–[79]33], the feeding and oviposition of P. micranthus still rely on M. micrantha [[80]34]. This finding may suggest that P. micranthus has evolved a potent detoxification ability to defend against xenobiotics from M. micranthus. The information on the P. micranthus genome will contribute to figuring out how this bug can resist its hosts’ defence. Invasive species have received worldwide attention, and they have caused severe economic loss and negative environmental impacts [[81]35]. There is already a multitude of methods to control invasive species, mainly including mechanical [[82]36], chemical [[83]37], and traditional biological control (introduce the natural enemies of invaders) [[84]38]. However, these methods are inefficient in controlling invasive species and cause diverse environmental impacts on ecosystems [[85]39]. The interactions between native or naturalized non-invasive and invasive species can prevent invasions [[86]40]. Furthermore, the co-evolution of native species and other local species matched with local phenology and will not limit non-target species. Therefore, using native species to control invasions could reduce the impact on non-target species and is expected to replace traditional biological control [[87]40, [88]41]. Using native insects to control invasive plants is effective and cost-efficient [[89]42]. Native insects can persist and reproduce naturally without excessive human intervention. The biological control agents and target species continuously adapt, making the development of resistance nearly impossible. This control method can also reduce chemical pesticides' short-term or long-term impacts on human health and the environment [[90]43, [91]44]. In general, P. micranthus, like other invertebrate biological control agents (both exotic and native), pose a shallow risk to human and animals, and there are virtually no reports of adverse effects in the literature [[92]45]. The side effects of other invertebrate biological control agents are limited to occasional bites, stings, and allergic reactions [[93]46], which have not been reported in P. micranthus. P. micranthus, a specialized and effective native enemy of M. micrantha [[94]1], belongs to the family Miridae, a species-rich family of plant bugs in Hemiptera, and contains an estimated 11,020 recorded species. Due to the broad range of food preferences and behaviours, mirid bugs can be divided into phytophagy,