Chromosome‐level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood)

The greenhouse whitefly, Trialeurodes vaporariorum Westwood, is an agricultural pest of global importance. Here we report a 787‐Mb high‐quality draft genome sequence of T. vaporariorum assembled from PacBio long reads and Hi‐C chromatin interaction maps, which has scaffold and contig N50 lengths of 70 Mb and 500 kb, respectively, and contains 18,275 protein‐coding genes. About 98.8% of the assembled contigs were placed onto the 11 T. vaporariorum chromosomes. Comparative genomic analysis reveals significantly expanded gene families such as aspartyl proteases in T. vaporariorum compared to Bemisia tabaci Mediterranean (MED) and Middle East‐Asia Minor 1 (MEAM1). Furthermore, the cytochrome CYP6 subfamily shows significant expansion in T. vaporariorum and several genes in this subfamily display developmental stage‐specific expression patterns. The high‐quality T. vaporariorum genome provides a valuable resource for research in a broad range of areas such as fundamental molecular ecology, insect–plant/insect–microorganism or virus interactions and pest resistance management.     

Preference of the vector thrips Frankliniella occidentalis for plants infected with thrips‐non‐transmissible Tomato spotted wilt virus

The effect of a thrips‐non‐transmissible Tomato spotted wilt virus (TSWV) on insect–host interactions between thrips and Arabidopsis thaliana was analysed. A wild‐type TSWV virulent isolate and a TSWV isolate that induces mild symptoms on inoculated plants (TSWV‐Mo) were used in this study, and TSWV‐Mo isolate was obtained by single local lesion isolation using Petunia x hybrid after several passages on Nicotiana rustica plants. In transmission test, although wild‐type TSWV (TSWV‐wt) was transmitted by two thrips species (transmission ratio; Frankliniella occidentalis, 25%; Thrips tabaci, 10%; and T. palmi, 0%), none of the thrips transmitted TSWV‐Mo. Feeding damage by F. occidentalis in A. thaliana plants was more extensive on TSWV‐wt‐infected plants than on TSWV‐Mo‐infected plants, despite comparable preference. Among the markers of plant defences, salicylic acid‐regulated genes were upregulated threefold to sixfold by TSWV‐wt or TSWV‐Mo infection. In contrast, jasmonate‐regulated genes and jasmonate/ethylene‐regulated genes were not affected by the infections. Pull assays showed that adjacent TSWV‐Mo‐infected plants were preferred over uninfected plants. In conclusion, our results showed that the transmissibility by thrips of TSWV is not related to preference of vector thrips and suggested that TSWV‐Mo‐infected plants may be used as attractants for behaviour control of thrips.     

In the presence of red light,cucumber and possibly other host plants lose their attractability to the melon thrips <Emphasis Type="Italic">Thrips palmi</Emphasis> (Thysanoptera: Thripidae)

The melon thrips, Thrips palmi Karny (Thysanoptera: Thripidae), is a serious agricultural pest of many crops. Previous studies have shown that red light decreases the number of Thrips palmi in greenhouses. In order to understand how red light affects T. palmi, we examined the behavioral responses to host plants that were irradiated with a red light-emitting diode panel (660 nm) in an environment with natural or fluorescent (normal-white) light. When T. palmi were allowed to move freely around in the experimental arena, we found that fewer individuals were attracted to plants irradiated by red light than to plants under normal light illumination. We then used a sticky trap of green coloration to exclude olfactory and visual stimuli associated with the host plants in order to test binary choice behavior in T. palmi. The number of thrips attracted to the green sticky trap irradiated with red light was approximately half of that without red light irradiation. This is the first study to show that an addition of red light can change the behavior of insects, leading to an avoidance of green targets in an environment of normal illumination.     

Time allocation of Orius sauteri in attacking Thrips palmi on an eggplant leaf

Orius sauteri (Poppius) (Heteroptera: Anthocoridae) is a polyphagous predator used as a biological control agent of palm thrips, Thrips palmi (Karny) (Thysanoptera: Thripidae). We studied O. sauteri's searching efficiency, time allocation on a leaf, leaving tendency, and attacking of prey. Approximately 78% of the encountered prey was eaten. Searching for prey was concentrated for 86% of the time on the lower leaf side, where palm thrips are usually found. Patch residence times on empty leaves were different from those on leaves with T. palmi larvae. Walking activity was not affected by the thrips density, and walking took place during 64% of the total search time. The leaving tendency of O. sauteri was affected by the time from patch entry and the presence or absence of palm thrips, but not by the thrips density. If prey were present, the leaving tendency decreased (multiplication factor 0.327), resulting in longer giving‐up times than when no prey was present. The fact that the leaving tendency increases when patch exploitation lasts longer suggests that not much time is wasted on patches where encounters with prey are scarce.     

Chromosome‐level genome assembly of the predator Propylea japonica to understand its tolerance to insecticides and high temperatures

The ladybird beetle Propylea japonica is an important natural enemy in agro‐ecological systems. Studies on the strong tolerance of P. japonica to high temperatures and insecticides, and its population and phenotype diversity have recently increased. However, abundant genome resources for obtaining insights into stress‐resistance mechanisms and genetic intra‐species diversity for P. japonica are lacking. Here, we constructed the P. japonica genome maps using Pacific Bioscience (PacBio) and Illumina sequencing technologies. The genome size was 850.90 Mb with a contig N50 of 813.13 kb. The Hi‐C sequence data were used to upgrade draft genome assemblies; 4,777 contigs were assembled to 10 chromosomes; and the final draft genome assembly was 803.93 Mb with a contig N50 of 813.98 kb and a scaffold N50 of 100.34 Mb. Approximately 495.38 Mb of repeated sequences was annotated. The 18,018 protein‐coding genes were predicted, of which 95.78% were functionally annotated, and 1,407 genes were species‐specific. The phylogenetic analysis showed that P. japonica diverged from the ancestor of Anoplophora glabripennis and Tribolium castaneum ~ 236.21 million years ago. We detected that some important gene families involved in detoxification of pesticides and tolerance to heat stress were expanded in P. japonica, especially cytochrome P450 and Hsp70 genes. Overall, the high‐quality draft genome sequence of P. japonica will provide invaluable resource for understanding the molecular mechanisms of stress resistance and will facilitate the research on population genetics, evolution and phylogeny of Coccinellidae. This genome will also provide new avenues for conserving the diversity of predator insects.     

Colonization of eucalypts in New Zealand by Australian insects

Since the 1860s, Australian insects have steadily colonized eucalypts in New Zealand. The rate of colonization has increased markedly over the last two decades. This increase may be related to increasing trade between the two countries. Currently there are 26 specialist eucalypt insect species and approximately 31 polyphagous insect species that can feed on Eucalyptus in New Zealand. The specialist eucalypt insects endemic to Australia have generally caused more damage than polyphagous or native insects. Eucalypt‐specific insects are dominated by sap sucking bugs, particularly psyllids, and defoliating Coleoptera and Lepidoptera. In some cases the major insect pest species have been those that are only occasional pests in Australia, for example Gonipterus scutellatus, Ctenarytaina eucalypti, Eriococcus coriaceus and Phylacteophaga froggatti. Some important insect pests have been rare, or even not described from Australia, prior to their appearance as a pest in New Zealand, for example Paropsis charybdis and Ophelimus eucalypti. Invading eucalypt insects are more likely to establish in the Auckland region than anywhere else in New Zealand.     

Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing,Bionano and Hi‐C technology

Onychostoma macrolepis is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome‐level assembly of the O.macrolepis genome obtained from the integration of nanopore long‐read sequencing with physical maps produced using Bionano and Hi‐C technology. A total of 87.9 Gb of nanopore sequence provided approximately 100‐fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi‐C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein‐coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non‐coding RNAs, in the genome. Evolutionary analysis revealed that O. macrolepis diverged from common carp approximately 24.25 million years ago. The chromosomes of O. macrolepis showed an unambiguous correspondence to the chromosomes of zebrafish. The high‐quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of O. macrolepis.     

Cold tolerance, overwintering and establishment potential of Thrips palmi

The cold tolerance and overwintering survival of the quarantine regulated pest and virus vector, Thrips palmi (Karny) (Thysanoptera: Thripidae), is examined and discussed in terms of its establishment potential in the U.K. Thrips palmi adults and first‐instar larvae have a wide distribution of supercooling points (SCPs) but show ‘pre‐freeze’ mortality as a result of both acute and chronic exposures to temperatures above the SCP range. Thrips palmi did not develop enhanced cold tolerance in response to cues previously shown to cold‐acclimate other thrips species. The acute cold tolerance of T. palmi is higher than that of the recently established and biologically similar species, Frankliniella occidentalis, which is thought to be capable only of very limited winter survival outdoors in the U.K. However, the more ecologically meaningful chronic assays reveal the opposite pattern. If introduced to the U.K., overwintering of T. palmi would thus be largely restricted to protected environments, as its cold tolerance is insufficient to permit outdoor survival for a complete winter. This assertion was demonstrated by caged populations that died out after as little as 25 days in outdoor winter conditions in Yorkshire, U.K. The reversal of relative tolerance of the two species when considering chronic and acute assays suggests that these forms of low temperature mortality have different physiological bases, and emphasizes the need to use both forms of assay in assessments of overwintering capacity.     

Chromosome‐level genome assembly of Triplophysa tibetana,a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Triplophysa is an endemic fish genus of the Tibetan Plateau in China. Triplophysa tibetana, which lives at a recorded altitude of ~4,000 m and plays an important role in the highland aquatic ecosystem, serves as an excellent model for investigating high‐altitude environmental adaptation. However, evolutionary and conservation studies of T. tibetana have been limited by scarce genomic resources for the genus Triplophysa. In the present study, we applied PacBio sequencing and the Hi‐C technique to assemble the T. tibetana genome. A 652‐Mb genome with 1,325 contigs with an N50 length of 3.1 Mb was obtained. The 1,137 contigs were further assembled into 25 chromosomes, representing 98.7% and 80.47% of all contigs at the base and sequence number level, respectively. Approximately 260 Mb of sequence, accounting for ~39.8% of the genome, was identified as repetitive elements. DNA transposons (16.3%), long interspersed nuclear elements (12.4%) and long terminal repeats (11.0%) were the most repetitive types. In total, 24,372 protein‐coding genes were predicted in the genome, and ~95% of the genes were functionally annotated via a search in public databases. Using whole genome sequence information, we found that T. tibetana diverged from its common ancestor with Danio rerio ~121.4 million years ago. The high‐quality genome assembled in this work not only provides a valuable genomic resource for future population and conservation studies of T. tibetana, but it also lays a solid foundation for further investigation into the mechanisms of environmental adaptation of endemic fishes in the Tibetan Plateau.     

A high‐quality chromosome‐level genome assembly of a generalist herbivore,Trichoplusia ni

The cabbage looper, Trichoplusia ni, is a globally distributed highly polyphagous herbivore and an important agricultural pest. T. ni has evolved resistance to various chemical insecticides, and is one of the only two insect species that have evolved resistance to the biopesticide Bacillus thuringiensis (Bt) in agricultural systems and has been selected for resistance to baculovirus infections. We report a 333‐Mb high‐quality T. ni genome assembly, which has N50 lengths of scaffolds and contigs of 4.6 Mb and 140 Kb, respectively, and contains 14,384 protein‐coding genes. High‐density genetic maps were constructed to anchor 305 Mb (91.7%) of the assembly to 31 chromosomes. Comparative genomic analysis of T. ni with Bombyx mori showed enrichment of tandemly duplicated genes in T. ni in families involved in detoxification and digestion, consistent with the broad host range of T. ni. High levels of genome synteny were found between T. ni and other sequenced lepidopterans. However, genome synteny analysis of T. ni and the T. ni derived cell line High Five (Hi5) indicated extensive genome rearrangements in the cell line. These results provided the first genomic evidence revealing the high instability of chromosomes in lepidopteran cell lines known from karyotypic observations. The high‐quality T. ni genome sequence provides a valuable resource for research in a broad range of areas including fundamental insect biology, insect‐plant interactions and co‐evolution, mechanisms and evolution of insect resistance to chemical and biological pesticides, and technology development for insect pest management.     

Predicting the potential geographic distribution of Thrips palmi in Korea,using the CLIMEX model

Thrips palmi Karny, melon thrips was introduced and first recorded in 1993 in Korea. This species has become a serious pest of vegetable and ornamental crops. The CLIMEX simulation was applied to T. palmi to predict its potential geographic distribution in Korea under the Representative Concentration Pathway (RCP) 8.5 climate change scenario. In the CLIMEX simulation, the ecoclimatic index was calculated, and compared in each simulated year and each simulated location. The map comparisons show good agreements between simulated and present distributions of T. palmi, indicating that the CLIMEX model has promising potential for prediction of future distributions of this species in Korea. In the near future, until the year 2020, all the western and eastern parts of Korea show favorable to marginal suitability for T. palmi populations in the fields. After the year 2040, potential distributions shift from no persistence to favorable for establishment and persistence from coastal to interior regions of the Korean peninsula, except for a north‐eastern interior region which is the northernmost part of a high mountainous (Baekdu‐Daegan) area in Korea. Based on the simulation results, the geographical distribution of T. palmi will expand over its current weather restrictions in the near future under a severe climate change scenario. Thus, pest management measures and strategies should be re‐evaluated in Korea, and should include further studies on interspecific competition and ecosystem changes due to climate changes.     

Ambrosiodmus rubricollis (Eichhoff) (Coleoptera; Curculionidae; Scolytinae) associated with young Tasmanian blue gum trees

Eucalypts are among the most widely planted forest trees in the world, and outside their native Australian range, the main arthropod pests are sap‐sucking insects, defoliators, gall‐making insects and xylophagous beetles. We report on a new association between a polyphagous wood‐boring beetle and Tasmanian blue gum (Eucalyptus globulus Labill.) in Central Portugal. Unidentified wood‐boring insects were found attacking two three‐year‐old E. globulus trees showing signs of decline among otherwise healthy trees in a commercial plantation, in June 2018. Declining trees presented dead twigs and branches, and recently developed epicormic sprouts evident on the trunks. Insects emerging from logs were identified as Ambrosiodmus rubricollis (Eichhoff), a species native to eastern and southern Asia, with the taxonomic identification validated by molecular analysis. To our knowledge, this is the first record of A. rubricollis associated with a eucalypt species worldwide. It is not clear whether the beetles played any significant role on the decline of the trees, but Ambrosiodmus may be potential pests for several tree and shrub species in Europe, as these beetles can transport pathogenic fungi.     

CRISPR/Cas9‐mediated mutagenesis of the white gene in the tephritid pest Bactrocera tryoni

The Queensland fruit fly, Bactrocera tryoni (Froggatt), is a polyphagous horticultural pest in Australia that is capable of causing significant damage to more than 100 different host fruits and vegetables. Chemical applications and ecological control strategies, such as the sterile insect technique (SIT), are commonly used to suppress established populations and eradicate invasive outbreaks following migration. The recently published B. tryoni draft genome provides new opportunities to identify candidate genes for targeted genome modification in order to generate advanced genetic strains for management using sterile insect strategies. Here, we demonstrate CRISPR/Cas‐mediated mutagenesis in B. tryoni through generating a series of frame‐shift mutations in the ATP‐dependent binding cassette transporter, white, causing a classic white‐eye phenotype. This work establishes methods for CRISPR/Cas genome editing in tephritids and demonstrates its potential for developing genetic sexing strains which could be used for SIT‐based pest control.     

Amount and time course of ingestion of plant subcellular fractions by two thrips and one reference mite species

Thrips are known as cell-feeding sucking pests, but little information is available on which and how much of each subcellular fraction they ingest. In this study, the ingested amounts of nuclei and plastids in two representative thrips species (the western flower thrips, Frankliniella occidentalis, and the garden thrips, Frankliniella intonsa) along with two reference sucking pests (the two-spotted spider mite, Tetranychus urticae, a cell feeder, and the brown planthopper, Nilaparvata lugens, a sap feeder) were quantified by quantitative PCR using phytoene desaturase and rubisco as respective marker genes following feeding. The ingested amounts of plastids were significantly greater than those of nuclei in the thrips and mite species. In the thrips species, however, the fold differences in ingested amount between the two fractions were substantially lower than their original ratio in intact plant cells, suggesting that thrips ingest nuclei more selectively than plastids. Unlike the thrips species, the ratio between nuclei and plastids increased in T. urticae. In contrast to these cell-feeding insects, no subcellular fraction was detected in N. lugens. These findings suggest that transgenic expression of foreign hairpin RNA in the nucleus would deliver a substantial amount of target molecules to cell-feeding sucking pests, but not sap-feeding pests, when employing ingestion RNA interference-based control strategies.     

Responses of five adult thrips species (Thysanoptera; Thripidae) to high-carbon dioxide atmospheres at different temperatures

The effect of high carbon dioxide atmospheres (60% CO₂) at different temperatures (20, 25, 30 and 34°C) on adult female mortality in Frankliniella occidentalis (Pergande), Frankliniella intonsa (Trybom), Thrips tabaci Lindeman, Thrips palmi Karny, and Thrips parvispinus Karny were tested. Mortality of the five thrips species increased with CO₂ exposure duration at each temperature. Median lethal times (LT₅₀) and times required to achieve 100% mortality due to CO₂ exposure decreased with increasing temperature, for all thrips species. Exposure to 60% CO₂ atmospheres at 30°C is considered to be 100% lethal within 24 h to most pests of fresh agricultural produce. Our findings suggest that CO₂ treatment could be used to propagate thrips-free plants in horticultural nurseries, and as a quarantine tool for controlling insects in/on transported plants.     

Detection of the Quarantine Species Thrips palmi by Loop-Mediated Isothermal Amplification

Thrips palmi (from the order Thysanoptera) is a serious insect pest of various crops, including vegetables, fruits and ornamental plants, causing significant economic losses. Its presence constitutes a double threat; not only does T. palmi feed on the plants, it is also a vector for several plant viruses. T. palmi originated in Asia, but has spread to North and Central America, Africa, Oceania and the Caribbean in recent decades. This species has been sporadically noted in Europe and is under quarantine regulation in the European Union. For non-specialists its larval stages are indistinguishable morphologically from another widespread and serious insect pest Frankliniella occidentalis (a non-quarantine species in the European Union) as well as other frequently occurring thrips. In this study, we have developed a loop-mediated isothermal amplification protocol to amplify rDNA regions of T. palmi. The results were consistent whether isolated DNA or crushed insects were used as template, indicating that the DNA isolation step could be omitted. The described method is species-specific and sensitive and provides a rapid diagnostic tool to detect T. palmi in the field.     

Silicon‐mediated resistance against specialist insects in sap‐sucking and leaf‐chewing guilds in the Si non‐accumulator collard

Soil amendment with Silicon (Si) can increase plant resistance against insect herbivores, but the underlying mechanisms remain unclear. The mechanical resistance hypothesis (MRH) states that Si accumulated in epidermal cells directly and passively protects against herbivores by creating a mechanical barrier. The physiological resistance hypothesis (PRH) states that Si enhances resistance by activating plant biochemical and physiological processes. We tested both hypotheses by manipulating Si fertilization of the Si non‐accumulator collard, Brassica oleracea L. cv. acephala (Brassicaceae). Then, we assessed functional and ultrastructural plant responses and the developmental and reproductive performance of the leaf‐chewing larvae of the diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae), and the sap‐sucking cabbage aphid, Brevicoryne brassicae L. (Hemiptera: Aphididae). There was a 20% increase in leaf Si content. Silicon deposition in epidermal cells was identified by confocal microscopy and directly coincided with lower performance of P. xylostella, but did not affect B. brassicae. On the other hand, we found no unequivocal evidence that Si‐mediated changes in primary and secondary metabolism improved plant resistance against the insects. Negative mechanical effects of Si on the insects may have masked beneficial effects of increased water, nitrogen, and mineral contents in Si‐treated collards. Silicon did not change leaf contents of hemicellulose, cellulose, and lignin. Although Si‐mediated increases in leaf glucosinolates (GLS) correlated with lower larval performance and higher oviposition preference of P. xylostella, both P. xylostella and B. brassicae are highly specialized in overcoming such secondary metabolites. Thus, mechanical resistance may have impaired P. xylostella, rather than the Si‐mediated increase in GLS. We suggest that the PRH may depend on the degree of insect feeding specialization, so that toxic Si‐mediated defenses may be more efficient against unadapted polyphagous herbivores. For them, a toxic barrier may be added to the mechanical resistance.     

Development of genomic resources for Nothofagus species using next‐generation sequencing data

Using next‐generation sequencing, we developed the first whole‐genome resources for two hybridizing Nothofagus species of the Patagonian forests that crucially lack genomic data, despite their ecological and industrial value. A de novo assembly strategy combining base quality control and optimization of the putative chloroplast gene map yielded ~32 000 contigs from 43% of the reads produced. With 12.5% of assembled reads, we covered ~96% of the chloroplast genome and ~70% of the mitochondrial gene content, providing functional and structural annotations for 112 and 52 genes, respectively. Functional annotation was possible on 15% of the contigs, with ~1750 potentially novel nuclear genes identified for Nothofagus species. We estimated that the new resources (13.41 Mb in total) included ~4000 gene regions representing ~6.5% of the expected genic partition of the genome, the remaining contigs potentially being nongenic DNA. A high‐quality single nucleotide polymorphisms resource was developed by comparing various filtering methods, and preliminary results indicate a strong conservation of cpDNA genomes in contrast to numerous exclusive nuclear polymorphisms in both species. Finally, we characterized 2274 potential simple sequence repeat (SSR) loci, designed primers for 769 of them and validated nine of 29 loci in 42 individuals per species. Nothofagus obliqua had more alleles (4.89) on average than N. nervosa (2.89), 8 SSRs were efficient to discriminate species, and three were successfully transferred in three other Nothofagus species. These resources will greatly help for future inferences of demographic, adaptive and hybridizing events in Nothofagus species, and for conserving and managing natural populations.     

Resistance to three thrips species in Capsicum spp. depends on site conditions and geographic regions

Capsicum species are commercially grown for pepper production. This crop suffers severely from thrips damage and the identification of natural sources of thrips resistance is essential for the development of resistant cultivars. It is unclear whether resistance to Frankliniella occidentalis as assessed in a specific environment holds under different conditions. Additionally, other thrips species may respond differently to the plant genotypes. Screening for robust and general resistance to thrips encompasses testing different Capsicum accessions under various conditions and with different thrips species. We screened 11 Capsicum accessions (C. annuum and C. chinense) for resistance to F. occidentalis at three different locations in the Netherlands. Next, the same 11 accessions were screened for resistance to Thrips palmi and Scirtothrips dorsalis at two locations in Asia. This resulted in a unique analysis of thrips resistance in Capsicum at five different locations around the world. Finally, all accessions were also screened for resistance to F. occidentalis in the Netherlands using a leaf disc choice assay, allowing direct comparison of whole plant and leaf disc assays. Resistance to F. occidentalis was only partially consistent among the three sites in the Netherlands. The most susceptible accessions were consistently susceptible, but which accession was the most resistant differed among sites. In Asia, one C. chinense accession was particularly resistant to S. dorsalis and T. palmi, but this was not the most resistant accession to F. occidentalis. Overall, resistance to F. occidentalis correlated with S. dorsalis but not with T. palmi resistance in the C. annuum accessions. Damage inflicted on leaf discs reflected damage on the whole plant level. Our study showed that identifying broad spectrum resistance to thrips in Capsicum may prove to be challenging. Breeding programmes should focus on developing cultivars suitable for growing in defined geographic regions with specific thrips species and abiotic conditions.