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

A near-complete genome assembly of Monochamus alternatus a major vector beetle of pinewood nematode

The Japanese sawyer beetle, Monochamus alternatus, is not only one of the most important wood boring pest itself, but also a major vector of the invasive pinewood nematode (PWN), which is the causal agent of the devastative pine wilt disease (PWD) and threats the global pine forest. Here, we present a near-complete genome of M. alternatus at the chromosome level. The assembled genome was 792.05 Mb with contig N50 length of 55.99 Mb, which is the largest N50 size among the sequenced Coleoptera insects currently. 99.57% of sequence was anchored onto ten pseudochromosomes (one X-chromosome and nine autosomes), and the final genome harbored only 13 gaps. BUSCO evaluation revealed the presence of 99.0% of complete core genes. Thus, our genome assembly represented the highest-contiguity genome assembly as well as high completeness in insects so far. We identified 20,471 protein-coding genes, of which 20,070 (98.04%) were functionally annotated. The genome assembly of M. alternatus provides a valuable resource for exploring the evolution of the symbiosis between PWN and the vector insects.

A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.

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.

A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect

BACKGROUND

Adaptations by arthropod pests to host plant defenses of crops determine their impacts on agricultural production. The larval host range of western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is restricted to maize and a few grasses. Resistance of D. v. virgifera to crop rotation practices and multiple insecticides contributes to its status as the most damaging pest of cultivated maize in North America and Europe. The extent to which adaptations by this pest contributes to host plant specialization remains unknown.

RESULTS

A 2.42 Gb draft D. v. virgifera genome, Dvir_v2.0, was assembled from short shotgun reads and scaffolded using long-insert mate-pair, transcriptome and linked read data. K-mer analysis predicted a repeat content of ≥ 61.5%. Ortholog assignments for Dvir_2.0 RefSeq models predict a greater number of species-specific gene duplications, including expansions in ATP binding cassette transporter and chemosensory gene families, than in other Coleoptera. A majority of annotated D. v. virgifera cytochrome P450s belong to CYP4, 6, and 9 clades. A total of 5,404 transcripts were differentially-expressed between D. v. virgifera larvae fed maize roots compared to alternative host (Miscanthus), a marginal host (Panicum virgatum), a poor host (Sorghum bicolor) and starvation treatments; Among differentially-expressed transcripts, 1,908 were shared across treatments and the least number were between Miscanthus compared to maize. Differentially-expressed transcripts were enriched for putative spliceosome, proteosome, and intracellular transport functions. General stress pathway functions were unique and enriched among up-regulated transcripts in marginal host, poor host, and starvation responses compared to responses on primary (maize) and alternate hosts.

CONCLUSIONS

Manual annotation of D. v. virgifera Dvir_2.0 RefSeq models predicted expansion of paralogs with gene families putatively involved in insecticide resistance and chemosensory perception. Our study also suggests that adaptations of D. v. virgifera larvae to feeding on an alternate host plant invoke fewer transcriptional changes compared to marginal or poor hosts. The shared up-regulation of stress response pathways between marginal host and poor host, and starvation treatments may reflect nutrient deprivation. This study provides insight into transcriptomic responses of larval feeding on different host plants and resources for genomic research on this economically significant pest of maize.

Nutritional and metabolic process of the dung beetle Phelotrupes auratus depends on the plant ingredients that the herbivores eat

Background

The dung beetle Phelotrupes auratus is a holometabolous insect belonging to the order Coleoptera, and it is widely distributed in Japan. The P. auratus habitat depends on herbivores. P. auratus eats the dung of the herbivores and carries it underground for its young. In this process, herbivore droppings disappear from the ground, not only keeping the ground hygienic but also maintaining good soil conditions for plant growth. In this way, a rich ecosystem is maintained. In recent years, the population of P. auratus has decreased, and the main cause has been the decrease in grazing land. It seems that Japanese dung beetles are mainly dependent on herbivores for nutrient sources. However, the physiological relationship between herbivores and P. auratus has not been well investigated. Here, we investigated the nutritional metabolism system of P. auratus by performing whole gene expression analysis of individuals collected from two areas where the ecosystem is occupied by different herbivores.

Results

We obtained 54,635 transcripts from P. auratus from Nara Park and Cape Toi and identified 2,592 differentially expressed genes in the fat bodies of the Nara Park and Cape Toi groups. We annotated P. auratus transcripts using Homo sapiens and Drosophila melanogaster genes as references; 50.5% of P. auratus transcripts were assigned to H. sapiens genes, and 54.0% of P. auratus transcripts were assigned to D. melanogaster genes. To perform gene set enrichment analysis, we chose H. sapiens genes for P. auratus transcript annotation. Principal component analysis and gene set enrichment analysis revealed that the nutritional metabolism of P. auratus from Cape Toi might differ from that of P. auratus from Nara Park.

Conclusion

We analyzed the nutritional metabolism system of P. auratus from Cape Toi and Nara Park and found that the characteristics of the nutritional metabolism process might depend on the plants consumed by the herbivores. Our findings will contribute to elucidating the relationships among habitat plants, herbivores, and dung decomposers and may aid in the maintenance of sustainable land health cycles.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08982-y.

Chromosome-level genome assembly of Monochamus saltuarius reveals its adaptation and interaction mechanism with pine wood nematode

Monochamus saltuarius (Coleoptera: Cerambycidae) was reported as the vector beetle of the pine wood nematode (PWN, Bursaphelenchus xylophilus) in Japan and Europe. It was first reported to transmitted the PWN to native Pinus species in 2018 in Liaoning Province, China. However, the lack of genomic resources has limited the in-depth understanding of its interspecific relationship with PWN. Here, we obtained a chromosome-level reference genome of M. saltuarius combining Illumina, Nanopore and Hi-C sequencing technologies. We assembled the scaffolds into ten chromosomes (including an X chromosome) and obtained a 682.23 Mb chromosome-level genome with a N50 of 73.69 Mb. In total, 427.67 Mb (62.69 %) repeat sequences were identified and 14, 492 protein-coding genes were predicted, of which 93.06 % were annotated. We described the mth/mthl, P450, OBP and OR gene families associated with the vector beetle's development and resistance, as well as the host selection and adaptation, which serve as a valuable resource for understanding the host adaptation in insects during evolution. This high quality reference genome of M. saltuarius also provide new avenues for researching the mechanism of this synergistic damage between vector beetles and PWN.

The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success

The lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), is a major global pest of cereal grains. Infestations are difficult to control as larvae feed inside grain kernels, and many populations are resistant to both contact insecticides and fumigants. We sequenced the genome of R. dominica to identify genes responsible for important biological functions and develop more targeted and efficacious management strategies. The genome was assembled from long read sequencing and long-range scaffolding technologies. The genome assembly is 479.1 Mb, close to the predicted genome size of 480.4 Mb by flow cytometry. This assembly is among the most contiguous beetle assemblies published to date, with 139 scaffolds, an N₅₀ of 53.6 Mb, and L₅₀ of 4, indicating chromosome-scale scaffolds. Predicted genes from biologically relevant groups were manually annotated using transcriptome data from adults and different larval tissues to guide annotation. The expansion of carbohydrase and serine peptidase genes suggest that they combine to enable efficient digestion of cereal proteins. A reduction in the copy number of several detoxification gene families relative to other coleopterans may reflect the low selective pressure on these genes in an insect that spends most of its life feeding internally. Chemoreceptor genes contain elevated numbers of pseudogenes for odorant receptors that also may be related to the recent ontogenetic shift of R. dominica to a diet consisting primarily of stored grains. Analysis of repetitive sequences will further define the evolution of bostrichid beetles compared to other species. The data overall contribute significantly to coleopteran genetic research.