De novo genome assembly of the white-spotted flower chafer (Protaetia brevitarsis)

Multiple Origins of Bioluminescence in Beetles and Evolution of Luciferase Function

Bioluminescence in beetles has long fascinated biologists, with diverse applications in biotechnology. To date, however, our understanding of its evolutionary origin and functional variation mechanisms remains poor. To address these questions, we obtained high-quality reference genomes of luminous and nonluminous beetles in 6 Elateroidea families. We then reconstructed a robust phylogenetic relationship for all luminous families and related nonluminous families. Comparative genomic analyses and biochemical functional experiments suggested that gene evolution within Elateroidea played a crucial role in the origin of bioluminescence, with multiple parallel origins observed in the luminous beetle families. While most luciferase-like proteins exhibited a conserved nonluminous amino acid pattern (TLA346 to 348) in the luciferin-binding sites, luciferases in the different luminous beetle families showed divergent luminous patterns at these sites (TSA/CCA/CSA/LVA). Comparisons of the structural and enzymatic properties of ancestral, extant, and site-directed mutant luciferases further reinforced the important role of these sites in the trade-off between acyl-CoA synthetase and luciferase activities. Furthermore, the evolution of bioluminescent color demonstrated a tendency toward hypsochromic shifts and variations among the luminous families. Taken together, our results revealed multiple parallel origins of bioluminescence and functional divergence within the beetle bioluminescent system.

A New Method for Discovering Plant Biostimulants

Structurally well-defined compounds have advantages for quality control in plant biostimulant production and application processes. Humic acid (HA) is a biostimulant that significantly affects plant growth, and soil-dwelling Protaetia brevitarsis larva (PBLs) can rapidly convert agricultural waste into HA. In this study, we use PBLs as a model to investigate HA formation and screen for structurally well-defined HA-related plant biostimulant compounds. Dephasing magic angle spinning nuclear magnetic resonance (13C DD-MAS NMR) analysis indicated HA structural changes during PBL digestion; metabolic profiling detected seven HA-related aromatic ring-containing compounds. A total of six compounds that significantly stimulate plant growth were identified through plant experiments, and all six compounds demonstrate the ability to enhance seed germination. It is noteworthy that piperic acid exhibits a remarkable promotion of root growth in plants, a finding reported for the first time in this study. Thus, this study not only provides insights into the insect-mediated transformation of HA but also illustrates a new method for discovering structurally well-defined plant biostimulant compounds.

Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure

BACKGROUND

Dastarcus helophoroides is an important natural enemy of cerambycids, and is wildly used in biological control of pests. Nevertheless, the absence of complete genomic information limits the investigation of the underlying molecular mechanisms. Here, a chromosome-level of Dastarcus helophoroides genome is assembled using a combination strategy of Illumina, PacBio, 10x™ Genomics, and Hi-C.

RESULTS

The final assembly is 609.09 Mb with contig N50, scaffold N50 and GC content of 5.46 Mb, 42.56 Mb and 31.50%, respectively, and 95.25% of the contigs anchor into 13 chromosomes. In total 14 890 protein-coding genes and 65.37% repeat sequences are predicted in the assembly genome. The phylogenetic analysis of single-copy gene families shared among 20 insect species indicates that Dastarcus helophoroides is placed as the sister species to clade (Nitidulidae+Curculionoidea+Chrysomeloidea) + Tenebrionoidea, and diverges from the related species ~242.9 Mya. In total 36 expanded gene families are identified in Dastarcus helophoroides genome, and are functionally related to drug metabolism and metabolism of xenobiotics by cytochrome P450. Some members of CYP4 Clade and CYP6 Clade are up-regulated in Dastarcus helophoroides adults upon insecticide exposure, of which expressions of DhCYP4Q, DhCYP6A14X1 and DhCYP4C1 are significantly up-regulated. The silencing of the three genes leads to adults more sensitive to insecticide and increased knocked-down rate, which may indicate their critical roles in stress resistance and detoxication.

CONCLUSION

Our study systematically integrated the chromosome-level genome, transcriptome and gene expression of Dastarcus helophoroides, which will provide valuable resources for understanding mechanisms of pesticide metabolism, growth and development, and utilization of the natural enemy in integrated control. © 2022 Society of Chemical Industry.

Identification and expression analyses of the olfactory-related genes in different tissues' transcriptome of a predacious soldier beetle, Podabrus annulatus (Coleoptera, Cantharidae)

We sequenced and analyzed the transcriptomes from different tissues of the soldier beetle, Podabrus annulatus (Coleoptera: Cantharidae), and obtained 75.74 Gb clean reads which were assembled into 95,274 unigenes. Among these transcripts, 25,484 unigenes of highly quality were annotated. Based on annotation and tBLASTn results, we identified a total of 101 candidate olfactory-related genes for the first time, including 11 putative odorant-binding proteins (OBPs), 6 chemosensory proteins (CSP), 50 olfactory receptors (ORs), 25 gustatory receptors (GRs), 6 ionotropic receptors (IRs), and 3 sensory neuron membrane proteins (SNMPs). BLASTX best-hit results indicated that these chemosensory genes were most identical to their respective orthologs from Photinus pyralis. Phylogenetic analyses also revealed that the ORs, GRs, and IRs of Podabrus annulatus are closely related to those of Photinus pyralis. The fragment per kilobase per million mapped fragments (FPKM) values showed that the PannOBP2, PannOBP3, and PannOBP10 were predominantly expressed in the antennae, PannOBP1 in the abdomen-thorax, while others were not identified to be tissue-specific. These olfactory-related differentially expressed genes (DEGs) demonstrated different roles in the olfactory system of Podabrus annulatus. This study establishes the groundwork for future research into the molecular mechanism of olfactory recognition in Podabrus annulatus.

Prediction and bioactivity of small-molecule antimicrobial peptides from Protaetia brevitarsis Lewis larvae

Antimicrobial peptides (AMPs) are widely recognized as promising natural antimicrobial agents. Insects, as the group of animals with the largest population, have great potential as a source of AMPs. Thus, it is worthwhile to investigate potential novel AMPs from Protaetia brevitarsis Lewis larvae, which is a saprophagous pest prevalent in China. In this study, comparing the whole-genome sequence of Protaetia brevitarsis Lewis larvae with the Antimicrobial Peptide Database (APD3) led to the identification of nine peptide templates that were potentially AMPs. Next, based on the peptide templates, 16 truncated sequences were predicted to the AMPs by bioinformatics software and then underwent structural and physicochemical property analysis. Thereafter, candidate small-molecule AMPs were artificially synthesized and their minimal inhibitory concentration (MIC) values were assessed. A candidate peptide, designated FD10, exhibited strong antimicrobial activity against both bacteria and fungi comprising Escherichia coli (MIC: 8 μg/mL), Pseudomonas aeruginosa (MIC: 8 μg/mL), Bacillus thuringiensis (MIC: 8 μg/mL), Staphylococcus aureus (MIC: 16 μg/mL), and Candida albicans (MIC: 16 μg/mL). Additionally, two other candidate peptides, designated FD12 and FD15, exhibited antimicrobial activity against both E. coli (MIC: both 32 μg/mL) and S. aureus (MIC: both 16 μg/mL). Moreover, FD10, FD12, and FD15 killed almost all E. coli and S. aureus cells within 1 h, and the hemolytic effect of FD10 (0.31%) and FD12 (0.40%) was lower than that of ampicillin (0.52%). These findings indicate that FD12, FD15, and especially FD10 are promising AMPs for therapeutic application. This study promoted the development of antibacterial drugs and provided a theoretical basis for promoting the practical application of antimicrobial peptides in the Protaetia brevitarsis Lewis larvae.

Transcriptome profiling for developmental stages Protaetia brevitarsis seulensis with focus on wing development and metamorphosis

A white-spotted flower chafer Protaetia brevitarsis seulensis widely distributed in Asian countries is traditionally used in oriental medicine. This study explored gene expression abundance with respect to wing development and metamorphosis in P. b. seulensis based on the large-scale RNA-seq data. The transcriptome assembly consists of 23,551 high-quality transcripts which are approximately 96.7% covered. We found 265 wing development genes, 19 metamorphosis genes, and 1,314 candidates. Of the 1,598 genes, 1,594 are included exclusively in cluster 4 with similar gene co-expression patterns. The network centrality analyses showed that wing development- and metamorphosis-related genes have a high degree of betweenness centrality and are expressed most highly in eggs, moderately in pupa and adults, and lowest in larva. This study provides some meaningful clues for elucidating the genetic modulation mechanism of wing development and metamorphosis in P. b. seulensis.

Transformation Capability Optimization and Product Application Potential of Proteatia brevitarsis (Coleoptera: Cetoniidae) Larvae on Cotton Stalks

Cotton stalks (CS) are a potential agricultural biomass resource. We investigated the use of CS as a feed for Proteatia brevitarsis Lewis larvae and the resulting frass (larvae dung-sand) as a fertilizer. Based on a three-factor experiment (decomposition inoculant, fermentation duration, and cattle manure ratio), the optimal parameters for the transformation of CS using P. brevitarsis larvae were determined as 40-50% of cattle manure, the use of VT inoculant and a fermentation duration of 25-30 days. Regarding the products of the transformation, the protein content of the larval body was as high as 52.49%, and the fat content was 11.7%, which is a suitable-quality insect protein source. The organic matter content of larvae dung-sand was 54.8%, and the content of total nitrogen, phosphorus, and potassium (TNPK) was 9.04%, which is twice more than that of the organic fertilizer standard (NY525-2021, Beijing, China, TNPK ≥ 4.0%), and larvae dung-sand has the potential of fertilizer application. Therefore, CS as a feed and fertilizer based on the transformation of P. brevitarsis larvae is feasible, and it is a highly efficient way to promote the utilization of both CS and cattle manure.

Microflora for improving the Auricularia auricula spent mushroom substrate for Protaetia brevitarsis production

Mushroom cultivation is a sustainable agricultural waste utilization method, but the lack of high-value utilization of the produced spent mushroom substrate (SMS) has hindered the development of mushroom cultivation-based circular agricultural systems. Conversion and utilization of SMS via Protaetia brevitarsis larvae (PBL) have proven to be a high-value AASMS utilization strategy. However, Auricularia auricula SMS (AASMS), which contains woodchips, is less palatable and digestible for PBL. To solve this problem, in this investigation, we screened out microflora (MF) for AASMS fermentation by comparing the fermentation performance as well as the effect on PBL feed intake, weight gain, and AASMS phytotoxic compound removal efficiency. In addition, by bacterial community analysis, the genera Luteimonas, Moheibacter, and Pseudoxanthomonas were predicted to be functional bacteria for AASMS fermentation and contribute to palatability and digestibility improvement.

•

Larvae frass microflora can ferment Auricularia auricula spent mushroom substrate

•

The fermentation can improve feed intake, weight gain, and phytotoxic removal efficiency

•

The genera Luteimonas, Moheibacter, and Pseudoxanthomonas were functional bacteria

Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line

BACKGROUND

The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study.

RESULTS

Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively.

CONCLUSIONS

This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.

Attenuation of antibiotic resistance genes in livestock manure through vermicomposting via Protaetia brevitarsis and its fate in a soil-vegetable system

Scarab larvae (Protaetia brevitarsis) could transform large quantities of agricultural waste into compost, providing a promising bio-fertilizer for soil management. There is an urgent need to assess the risk of antibiotic resistance genes (ARGs) in soil-vegetable system with application of compost derived from P. brevitarsis larvae. We conducted a pot experiment to compare the changes of ARGs in the soil and lettuce by adding four types of manure, livestock manure (chicken and swine manure) and the corresponding larval frass. Significantly low numbers of ARGs and mobile genetic elements (MGEs) were detected in both larval frass compared with the corresponding livestock manure. Pot experiment showed that the detected numbers of ARGs and MGEs in bulk soil, rhizosphere soil, and root endophytes were significantly lower in the frass-amended treatments than the raw manure-amended treatments. Furthermore, the relative abundance of ARGs and MGEs with application of chicken-frass was significant lower in rhizosphere soil and leaf endophyte. Using non-metric multidimensional scaling analysis, the patterns of soil ARGs and MGEs with chicken-frass application were more close to those from the bulk soil in the control. Structural equation models indicated that livestock manure addition was the main driver shaping soil ARGs with raw manure application, while MGEs were the key drivers in frass-amended treatments. These findings demonstrated that application of livestock manure vermicomposting via scarab larvae (P. brevitarsis) may be at low risk in spreading manure-borne ARGs through soil-plant system, providing an alternative technique for reducing ARGs in organic waste.

Characterization of Microorganisms from Protaetia brevitarsis Larva Frass

Decomposers play an important role in the biogeochemical cycle. Protaetia brevitarsis larvae (PBLs) can transform wastes into frass rich in humic acid (HA) and microorganisms, which may increase the disease resistance of plants and promote plant growth. Beyond HA, the microorganisms may also contribute to the biostimulant activity. To address this hypothesis, we investigated the potential microbial community in the PBL frass samples and elucidated their functions of disease resistance and plant growth promotion. High-throughput sequencing analysis of four PBL-relevant samples showed that their frass can influence the microbial community of the surrounding environment. Further analysis showed that there were many microorganisms beneficial to agriculture, such as Bacillus. Therefore, culturable Bacillus microbes were isolated from frass, and 16S rDNA gene analysis showed that Bacillus subtilis was the dominant species. In addition, some Bacillus microorganisms isolated from the PBL frass had antibacterial activities against pathogenic fungi. The plant growth promotion pot experiment also proved that some strains promote plant growth. In conclusion, this study demonstrated that the microorganisms in the PBL frass are conducive to colonizing the surrounding organic matrix, which will help beneficial microbes to increase the disease resistance of plants and promote plant growth.

Digestibility of insect meals for Pacific white shrimp (Litopenaeus vannamei) and their performance for growth, feed utilization and immune responses

This study was conducted to examine digestibility of insect meals for Pacific white shrimp (Litopenaeus vannamei) and their utilization as fish meal substitutes. The tested insect meals were mealworm, silkworm, black soldier fly, rice grasshopper, two-spotted cricket, dynastid beetle and white-spotted flower chafer. Apparent digestibility coefficients of the tested insect meals were 83-89% for protein, 91-98% for lipid, 84-90% for energy, 77-81% for dry matter, 28-36% for chitin, 76-96% for amino acids and 89-93% for fatty acids. The amino acid availability of insect meals was high in taurine (93-96%), arginine (91-95%) and lysine (90-95%). Availability of fatty acids were 89-93% for saturated fatty acids, 90-93% for monounsaturated fatty acids and 88-93% for polyunsaturated fatty acids. For a feeding trial, a control diet was formulated using 27% tuna byproduct meal as a fish meal source and seven other diets were prepared replacing 10% tuna byproduct meal in the control diet with each insect meal. Triplicate groups of shrimp (initial body weight: 0.17 g) were fed the diets for 65 days. The growth performance was significantly improved when the shrimp were fed black soldier fly or dynastid beetle included diet. Dietary supplementation of insect meals significantly improved non-specific immune responses and antioxidant enzyme activity in the shrimp. These results indicate that the tested insect meals have high potentials to be used as a protein source that could replace fish meal in diets for the shrimp.

Identification and field verification of an aggregation pheromone from the white-spotted flower chafer, Protaetia brevitarsis Lewis (Coleoptera: Scarabaeidae)

The white-spotted flower chafer (WSFC), Protaetia brevitarsis Lewis, is native to East Asia. Although their larvae are considered a potential resource insect for degrading plant residues, producing protein fodder, and processing to traditional medicine, adult WSFCs inflict damage to dozens of fruit and economic crops. The control of the WSFC still relies heavily on pesticides and the inefficient manual extraction of adults. Here, we report the identification and evaluation of the aggregation pheromone of WSFCs. From the headspace volatiles emitted from WSFC adults, anisole, 4-methylanisole, 2-heptanone and 2-nonanone were identified as WSFC-specific components. However, only anisole and 4-methylanisole elicited positive dose-response relationship in electroantennography tests, and only 4-methylanisole significantly attracted WSFCs of both sexes in olfactometer bioassays and field experiments. These results concluded that 4-methylanisole is the aggregation pheromone of WSFCs. Furthermore, we developed polyethylene vials as long-term dispensers of 4-methylanisole to attract and kill WSFCs. The polyethylene vial lures could effectively attracted WSFCs for more than four weeks. Pheromone-based lures can be developed as an environmentally friendly protocol for monitoring and controlling WSFC adults.

Characterizing the Role of Orco Gene in Detecting Aggregation Pheromone and Food Resources in Protaetia brevitarsis Leiws (Coleoptera: Scarabaeidae)

An accurate olfactory system for recognizing semiochemicals and environmental chemical signals plays crucial roles in survival and reproduction of insects. Among all olfaction-related proteins, olfactory receptors (ORs) contribute to the conversion of chemical stimuli to electric signals and thereby are vital in odorant recognition. Olfactory receptor co-receptor (Orco), one of the most conserved ORs, is extremely essential in recognizing odorants through forming a ligand-gated ion channel complex with conventional ligand-binding odorant receptors. We have previously identified aggregation pheromone in Protaetia brevitarsis (Coleoptera: Scarabaeidae), a native agricultural and horticultural pest in East-Asia. However, to our best knowledge, its olfaction recognition mechanisms are still veiled. To illustrate how P. brevitarsis recognize aggregation pheromone and host plants, in the present study we cloned and sequenced the full-length Orco gene from P. brevitarsis antennae (named PbreOrco) and found that PbreOrco is highly conserved and similar to Orcos from other Coleoptera insects. Our real-time quantitative PCR (qRT-PCR) results showed that PbreOrco is mainly expressed in antenna. We also demonstrated that silencing PbreOrco using RNA interference through injecting dsOrco fragment significantly inhibited PbreOrco expression in comparison with injecting control dsGFP and subsequently revealed using electroantennogram and behavioral bioassays that decreasing PbreOrco transcript abundance significantly impaired the responses of P. brevitarsis to intraspecific aggregation pheromone and prolonged the time of P. brevitarsis spending on food seeking. Overall, our results demonstrated that PbreOrco is crucial in mediating odorant perception in P. brevitarsis.

The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)

BACKGROUND

Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far.

RESULTS

The genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation.

CONCLUSIONS

The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.

Drug Discovery Insights from Medicinal Beetles in Traditional Chinese Medicine

Traditional Chinese medicine (TCM) was the primary source of medical treatment for the people inhabiting East Asia for thousands of years. These ancient practices have incorporated a wide variety of materia medica including plants, animals and minerals. As modern sciences, including natural products chemistry, emerged, there became increasing efforts to explore the chemistry of this materia medica to find molecules responsible for their traditional use. Insects, including beetles have played an important role in TCM. In our survey of texts and review articles on TCM materia medica, we found 48 species of beetles from 34 genera in 14 different families that are used in TCM. This review covers the chemistry known from the beetles used in TCM, or in cases where a species used in these practices has not been chemically studied, we discuss the chemistry of closely related beetles. We also found several documented uses of beetles in Traditional Korean Medicine (TKM), and included them where appropriate. There are 129 chemical constituents of beetles discussed.

A review of deep learning applications for genomic selection

BACKGROUND

Several conventional genomic Bayesian (or no Bayesian) prediction methods have been proposed including the standard additive genetic effect model for which the variance components are estimated with mixed model equations. In recent years, deep learning (DL) methods have been considered in the context of genomic prediction. The DL methods are nonparametric models providing flexibility to adapt to complicated associations between data and output with the ability to adapt to very complex patterns.

MAIN BODY

We review the applications of deep learning (DL) methods in genomic selection (GS) to obtain a meta-picture of GS performance and highlight how these tools can help solve challenging plant breeding problems. We also provide general guidance for the effective use of DL methods including the fundamentals of DL and the requirements for its appropriate use. We discuss the pros and cons of this technique compared to traditional genomic prediction approaches as well as the current trends in DL applications.

CONCLUSIONS

The main requirement for using DL is the quality and sufficiently large training data. Although, based on current literature GS in plant and animal breeding we did not find clear superiority of DL in terms of prediction power compared to conventional genome based prediction models. Nevertheless, there are clear evidences that DL algorithms capture nonlinear patterns more efficiently than conventional genome based. Deep learning algorithms are able to integrate data from different sources as is usually needed in GS assisted breeding and it shows the ability for improving prediction accuracy for large plant breeding data. It is important to apply DL to large training-testing data sets.

Characterization and analysis of the transcriptome in Opisina arenosella from different developmental stages using single-molecule real-time transcript sequencing and RNA-seq

Opisina arenosella is one of the main pests harming coconut trees. To date, there have been few studies on the molecular genetics, biochemistry and physiology of O. arenosella at the transcriptional level, and there are no available reference genomes. Here, Illumina RNA sequencing combined with PacBio single-molecule real-time analysis was applied to study the transcriptome of this pest at different developmental stages, providing reference data for transcript expression analysis. Twelve samples of O. arenosella from different stages of development were sequenced using Illumina RNA sequencing, and the pooled RNA samples were sequenced with PacBio technology (Iso-Seq). A full-length transcriptome with 41,938 transcripts was captured, and the N50 and N90 lengths were 3543 bp and 1646 bp, respectively. A total of 36,925 transcripts were annotated in public databases, 6493 of which were long noncoding RNAs, while 2510 represented alternative splicing events. There were significant differences in the gene expression profiles at different developmental stages, with high levels of differential gene expression associated with growth, development, carbohydrate metabolism and immunity. This work provides resources and information for the study of the transcriptome and gene function of O. arenosella and provides a valuable foundation for understanding the changes in gene expression during development.

A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

BACKGROUND

A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region.

RESULTS

The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig.

CONCLUSIONS

We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.