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

Microinjection-enabled gene silencing in first instar larvae of western flower thrips, Frankliniella occidentalis, reveals vital genes for larval survival

The western flower thrips (Frankliniella occidentalis) is a significant agricultural pest, causing severe global yield losses due to extensive feeding damage and the transmission of plant pathogenic viruses. Despite recent advancements in RNA interference (RNAi) in thrips species, its application has been mostly limited to the adult stage. Given the crucial role of first instar larval thrips in acquiring and transmitting orthotospoviruses, achieving gene silencing in these larvae is critical for studying virus entry and acquisition. While thoracic and abdominal injections have proven effective in adult thrips, the low post-injection survival rate hinders their use in larval thrips. This study addresses this challenge by presenting a microinjection methodology to deliver dsRNA into the hemolymph of first instar larval thrips through the coxa, the first proximal segment of the foreleg. This method significantly improved larval survival rate by preventing detrimental damage to the internal tissues. Significant knockdown of V-ATPase-B, cytochrome P450 (CYP3653A2), and apolipophorin-II/I (ApoLp-II/I) transcripts was confirmed after 48 and/or 72 h post injection (hpi), corresponding to the first and second instar larval stages, respectively. Silencing CYP3653A2 or ApoLp-II/I significantly increased larval mortality. These findings demonstrate proof-of-principle of gene silencing and associated silencing phenotype (mortality) for first instar larval thrips and highlight the essential role of CYP3653A2 and ApoLp-II/I in larval vitality. Our RNAi-based tool offers an opportunity to investigate the molecular mechanisms of thrips-orthotospovirus interactions, as the virus must be acquired by young larval thrips for successful transmission to plants, thus presenting potential targets for thrips pest management.

Chromosome-level genome assembly of Cyamophila willieti (Hemiptera: Psyllidae)

Cyamophila willieti (Hemiptera: Psyllidae) is a significant pest that adversely affects the growth of Styphnolobium japonicum and its variant, Styphnolobium japonicum f. pendula. Despite its impact, research on this species remains limited. In this study, we successfully assembled a chromosome-level genome for Cyamophila willieti using a comprehensive approach that integrated Illumina sequencing, PacBio sequencing, and Hi-C technology. The genome size was determined to be 361.61 Mb, with a scaffold N50 length of 28.90 Mb. Additionally, the genome was mapped to 13 chromosomes (N = 12 A + X), and a total of 15,841 genes were predicted, with 90.38% of them functionally annotated. In summary, the high-quality genome of Cyamophila willieti provides valuable data to support further research, including pest management strategies.

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.

Chromosome-level genome assembly of the western flower thrips Frankliniella occidentalis

The western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) is a global invasive species that causes increasing damage by direct feeding on crops and transmission of plant viruses. Here, we assemble a previously published scaffold-level genome into a chromosomal level using Hi-C sequencing technology. The assembled genome has a size of 302.58 Mb, with a contig N50 of 1533 bp, scaffold N50 of 19.071 Mb, and BUSCO completeness of 97.8%. All contigs are anchored on 15 chromosomes. A total of 16,312 protein-coding genes are annotated in the genome with a BUSCO completeness of 95.2%. The genome contains 492 non-coding RNA, and 0.41% of interspersed repeats. In conclusion, this high-quality genome provides a convenient and high-quality resource for understanding the ecology, genetics, and evolution of thrips.

Chromosome-level genome assembly of Odontothrips loti Haliday (Thysanoptera: Thripidae)

As the predominant pest of alfalfa, Odontothrips loti Haliday causes great damages over the major alfalfa-growing regions of China. The characteristics of strong mobility and fecundity make them develop rapidly in the field and hard to be controlled. There is a shortage of bioinformation and limited genomic resources available of O. loti for us to develop novel pest management strategies. In this study, we constructed a chromosome-level reference genome assembly of O. loti with a genome size of 346.59 Mb and scaffold N50 length of 18.52 Mb, anchored onto 16 chromosomes and contained 20128 genes, of which 93.59% were functionally annotated. The results of 99.20% complete insecta_odb10 genes in BUSCO analysis, 91.11% short reads mapped to the ref-genome, and the consistent tendency among the thrips in the distribution of gene length reflects the quality of genome. Our study provided the first report of genome for the genus Odontothrips, which offers a genomic resource for further investigations on evolution and molecular biology of O. loti, contributing to pest management.

Mutation V65I in the β1 Subunit of the Nicotinic Acetylcholine Receptor Confers Neonicotinoid and Sulfoxaflor Resistance in Insects

Neonicotinoids have been widely used to control pests with remarkable effectiveness. Excessive insecticides have led to serious insect resistance. Mutations of the nicotinic acetylcholine receptor (nAChR) are one of the reasons for neonicotinoid resistance conferred in various agricultural pests. Two mutations, V65I and V104I, were found in the nAChR β1 subunit of two neonicotinoid-resistant aphid populations. However, the specific functions of the two mutations remain unclear. In this study, we cloned and identified four nAChR subunits (α1, α2, α8, and β1) of thrips and found them to be highly homologous to the nAChR subunits of other insects. Subsequently, we successfully expressed two subtypes nAChR (α1/α2/α8/β1 and α1/α8/β1) by coinjecting three cofactors for the first time in thrips, and α1/α8/β1 showed abundant current rapidly. Acetylcholine, neonicotinoids, and sulfoxaflor exhibited different activation capacities for the two subtypes of nAChRs. Finally, V65I was found to significantly reduce the binding ability of nAChR to neonicotinoids and sulfoxaflor through electrophysiology and computer simulations. V104I caused a decrease in agonist affinity (pEC50) but an increase in the efficacy (Imax) of nAChR against neonicotinoids and reduced the binding ability of nAChR to sulfoxaflor. This study provides theoretical and technical support for studying the molecular mechanisms of neonicotinoid resistance in pests.

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.

Chromosome-level genome of spider Pardosa pseudoannulata and cuticle protein genes in environmental stresses

Spiders are representative arthropods of adaptive radiation. The high-quality genomes have only been reported in several web weaver spider species, leaving the wandering spiders' genomic information scarce. The pond wolf spider, Pardosa pseudoannulata, is a representative species in the retrolateral titial apophysis (RTA) clade. We present a chromosome-level P. pseusoannulata genome assembly of 2.42 Gb in size with a scaffold N50 of 169.99 Mb. Hi-C scaffolding assigns 94.83% of the bases to 15 pseudo-chromosomes. The repeats account for 52.79% of the assembly. The assembly includes 96.2% of the complete arthropod universal single-copy orthologs. Gene annotation predicted 24,530 protein-coding genes with a BUSCO score of 95.8% complete. We identified duplicate clusters of Hox genes and an expanded cuticle protein gene family with 243 genes. The expression patterns of CPR genes change in response to environmental stresses such as coldness and insecticide exposure. The high-quality P. pseudoannulata genome provides valuable information for functional and comparative studies in spiders.

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.