The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology

A high-quality chromosome-level genome assembly of the mulberry looper, Phthonandria atrilineata

The mulberry looper (Phthonandria atrilineata), a geometrid moth, plays a pivotal role in the destruction of mulberry trees (Morus spp.). In China, P. atrilineata is the most significant insect pest to sericulture, as it feeds on mulberry leaves and spreads diseases. The outbreak trend of P. atrilineata has been expanding yearly, causing substantial economic losses. Despite its ecological and economic importance, knowledge about the genomic background of P. atrilineata remains limited. Here, we report a chromosome-level reference genome of P. atrilineata, with a total size of 336.55 Mb, containing 15,026 protein-coding genes and 39.72% repeat sequences. These findings have the potential to shed light on the genetic basis of the destructive nature and environmental adaptation of P. atrilineata, offering valuable genomic resources for understanding genome evolution and pest management within this Lepidopteran pest.

Characterization of sulfakinin and its role in larval feeding and molting in Spodoptera frugiperda

Feeding and molting are particularly important physiological processes for insects, and it has been reported that neuropeptides are involved in the nervous regulation of these 2 processes. Sulfakinin (SK) is an important neuropeptide that is widely distributed among insects and plays a pivotal role in regulating feeding, courtship, aggression, and locomotion. In this study, we investigated the involvement of SK in feeding and molting on a highly notorious pest insect, the fall armyworm, Spodoptera frugiperda. SK transcript levels were found in all larval stages and there was a predominant expression of SK in the brain of 5th instar larvae. By immunostaining, SK was detected in 2 pairs of cells in the median protocerebrum. But during prolonged periods of starvation, there was a significant reduction in SK messenger RNA levels; however, subsequent refeeding led to a notable increase. To investigate the role of SK in feeding and molting, SK was silenced in S. frugiperda larvae through RNA interference. This resulted in a significant increase in food intake, weight gain, and the molting process happened more rapidly in the double-stranded SK-treated larvae compared to the controls. Conversely, injection of sulfated SK peptide (sSK) caused opposite effects. Interestingly, SK-knockdown in larvae resulted in increased levels of 20-hydroxyecdysone and also of the expression of some of it signaling pathway genes. Altogether, this study highlights the important role played by SK in regulating feeding and molting in S. frugiperda.

The T2T Genome of the Domesticated Silkworm Bombyx mori

Genome sequences contain the fundamental genetic information that largely determines the biology of a species. Over the past 20 years, advancements in high-throughput sequencing technologies and bioinformatics tools have matured, facilitating genome assembly and ushering in the telomere-to-telomere (T2T) era. Bombyx mori is renowned as a silk-producing insect and serves as an important model organism extensively studied across various fields of biology. In this study, we present the first assembled T2T genome by integrating HiFi, ultra-long ONT, NGS, and Hi-C data. This assembly comprises 450,267,439 base pairs from 28 chromosomes and includes annotations for a total of 18,253 protein-coding genes. A completeness evaluation revealed that 99.1% of conserved single-copy genes were included, as determined by a BUSCO analysis. Furthermore, the consensus quality (QV) assessed through Merqury was recorded at 59.88. The proportion of repeat sequence achieved 60.77%, marking it as the highest reported value for B. mori to date. In comparison to previously published genomes, our assembly offers a more complete and higher quality representation, particularly concerning highly homologous tandem regions such as telomeres, rDNA clusters, and Gr family regions. Furthermore, our extensive experience in genome assembly, including sample preparation experience and assembly strategies to reduce complexity, will provide valuable references for other species aiming to achieve their own T2T genome assemblies.

Comparative genomic and phylogenetic analysis of the complete mitochondrial genome of Cricula trifenestrata (Helfer) among lepidopteran insects

Cricula trifenestrata Helfer (commonly known as Amphutukoni muga/Cricula silkworm), a wild sericigenous insect produces golden yellow silk similar to Antheraea assamensis (muga silkworm), with significant potential as a natural fiber and biomaterial. Cricula is considered as a pest as it competes for food with muga, which produces the prized golden silk. This study focuses on decoding the mitochondrial genome of C. trifenestrata using next-generation sequencing technology and includes comparative analysis with Bombycoids and other lepidopteran insects. We found that the Cricula mitogenome spans 15 425 bp and exhibits typical gene content and arrangement consistent with other Saturniids and lepidopterans. All protein-coding genes were found to undergo purifying selection, with the highest and lowest conservation observed in the cox1 and atp8 gene, respectively, indicating their potential role in future evolutionary events. We identified two types of mismatches: 23 "G-U" and 6 "U-U" pairs, similar to those found in Actias selene among the Saturniids. Additionally, our study uncovered the presence of two 33 bp repeat units and a "TTAGA" motif in the control region, in contrast to the typical "ATAGA" motif, suggesting functional similarity with evolving sequences. Furthermore, phylogenetic analysis supports the close relationship of Cricula with other species within the Saturniidae family.

Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea)

The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.

Tracking Adaptive Pathways of Invasive Insects: Novel Insight from Genomics

Despite the huge human and economic costs of invasive insects, which are the main group of invasive species, their environmental impacts through various mechanisms remain inadequately explained in databases and much of the invasion biology literature. High-throughput sequencing technology, especially whole-genome sequencing, has been used as a powerful method to study the mechanisms through which insects achieve invasion. In this study, we reviewed whole-genome sequencing-based advances in revealing several important invasion mechanisms of invasive insects, including (1) the rapid genetic variation and evolution of invasive populations, (2) invasion history and dispersal paths, (3) rapid adaptation to different host plant ranges, (4) strong environmental adaptation, (5) the development of insecticide resistance, and (6) the synergistic damage caused by invasive insects and endosymbiotic bacteria. We also discussed prevention and control technologies based on whole-genome sequencing and their prospects.

CRISPR/Cas9-mediated methoprene-tolerant 1 knockout results in precocious metamorphosis of beet armyworm (Spodoptera exigua) only at the late larval stage

Juvenile hormone (JH) controls almost every aspect of an insect, especially metamorphosis. Since RNA interference works on transcripts and is often insufficient in Lepidoptera, how JH affects larval development in these insects is not well studied. Using the CRISPR/Cas9 technique, we knocked out Spodoptera exigua methoprene-tolerant 1 (SeMet1) gene of beet armyworm by modifying two sites in the coding region. However, SeMet1 knockout did not affect egg hatch rate or larval development at L1-L3 stages. In contrast to the consistent five larval instars of the control group, L4 SeMet1 mutants began to show signs of precocious metamorphosis, that is, small patches of pupal cuticle. Most L4 and all L5 SeMet1 mutants died for failing to shed their mosaic cuticles. RNA-seq indicated that most genes encoding pupal cuticle proteins and chitinase genes were altered in SeMet1 mutant L4 larvae. SeKr-h1, a key transcription factor in JH action was significantly down-regulated in L3-L5 larvae, while SeBR-C, a pupal indicator was only upregulated in L4-L5 larvae. These results suggested that S. exigua larvae may initially develop independently of JH, and involve SeMet1 in transducing JH signalling, leading to controlled larval metamorphosis at the late larval stage. We believe our findings will enhance better understanding of JH regulation of larval development.

Methoprene-tolerant and Krüppel homolog 1 are actors of juvenile hormone-signaling controlling the development of male sexual behavior in the moth Agrotis ipsilon

In insects, juvenile hormone (JH) is critical for the orchestration of male reproductive maturation. For instance, in the male moth, Agrotis ipsilon, the behavioral response and the neuronal sensitivity within the primary olfactory centers, the antennal lobes (ALs), to the female-emitted sex pheromone increase with fertility during adulthood and the coordination between these events is governed by JH. However, the molecular basis of JH action in the development of sexual behavior remains largely unknown. Here, we show that the expression of the paralogous JH receptors, Methoprene-tolerant 1 and 2 (Met1, Met2) and of the JH-inducible transcription factor, Krüppel homolog 1 (Kr-h1) within ALs raised from the third day of adult life and this dynamic is correlated with increased behavioral responsiveness to sex pheromone. Met1-, Met2- and Kr-h1-depleted sexually mature males exhibited altered sex pheromone-guided orientation flight. Moreover, injection of JH-II into young males enhanced the behavioral response to sex pheromone with increased AL Met1, Met2 and Kr-h1 mRNA levels. By contrast, JH deficiency suppressed the behavioral response to sex pheromone coupled with reduced AL Met1, Met2 and Kr-h1 mRNA levels in allatectomized old males and these inhibitions were compensated by an injection of JH-II in operated males. Our results demonstrated that JH acts through Met-Kr-h1 signaling pathway operating in ALs, to promote the pheromone information processing and consequently the display of sexual behavior in synchronization with fertility to optimize male reproductive fitness. Thus, this study provides insights into the molecular mechanisms underlying the hormonal regulation of reproductive behavior in insects.

Accumulation of retrotransposons contributes to W chromosome differentiation in the willow beauty Peribatodes rhomboidaria (Lepidoptera: Geometridae)

The W chromosome of Lepidoptera is typically gene-poor, repeat-rich and composed of heterochromatin. Pioneering studies investigating this chromosome reported an abundance of mobile elements. However, the actual composition of the W chromosome varies greatly between species, as repeatedly demonstrated by comparative genomic hybridization (CGH) or fluorescence in situ hybridization (FISH). Here we present an analysis of repeats on the W chromosome in the willow beauty, Peribatodes rhomboidaria (Geometridae), a species in which CGH predicted an abundance of W-enriched or W-specific sequences. Indeed, comparative analysis of male and female genomes using RepeatExplorer identified ten putative W chromosome-enriched repeats, most of which are LTR or LINE mobile elements. We analysed the two most abundant: PRW LINE-like and PRW Bel-Pao. The results of FISH mapping and bioinformatic analysis confirmed their enrichment on the W chromosome, supporting the hypothesis that mobile elements are the driving force of W chromosome differentiation in Lepidoptera. As the W chromosome is highly underrepresented in chromosome-level genome assemblies of Lepidoptera, this recently introduced approach, combining bioinformatic comparative genome analysis with molecular cytogenetics, provides an elegant tool for studying this elusive and rapidly evolving part of the genome.

Dipteran endoparasitoid Exorista bombycis utilizes antihemocyte components against host defense of silkworm Bombyx mori

Dipteran endoparasitoids avoid host immune response; however, antidefense components from the Dipterans are unknown. Infestation of commercial silkworm Bombyx mori Linnaeus (Lepidoptera: Bombycidae) by endoparasitoid Exorista bombycis Louis (Diptera: Tachinidae) induced immune reactions, cytotoxicity, granulation, degranulation, and augmented release of cytotoxic marker enzyme lactate dehydrogenase (LDH), and degranulation-mediator enzyme β-hexosaminidase in hemocytes. In this study, by reverse phase high-performance liquid chromatography, fractions of E. bombycis larval tissue protein with antihemocytic activity are separated. From the fraction, peptides of hemocyte aggregation inhibitor protein (HAIP) and pyridoxamine phosphate oxidase (PNPO) are identified by mass spectrometry. Interacting partners of HAIP and PNPO are retrieved that further enhance the virulence of the parasitoid. PNPO and HAIP genes showed a four- to seven fold increase in expression in the integument of the parasitoid larva. Together, the dipteran endoparasitoid E. bombycis exploit antihemocyte activity to inhibit host defense reactions in addition to defense evasion contemplated.

Transcriptional regulation underlying the temperature response of embryonic development rate in the winter moth

Climate change will strongly affect the developmental timing of insects, as their development rate depends largely on ambient temperature. However, we know little about the genetic mechanisms underlying the temperature sensitivity of embryonic development in insects. We investigated embryonic development rate in the winter moth (Operophtera brumata), a species with egg dormancy which has been under selection due to climate change. We used RNA sequencing to investigate which genes are involved in the regulation of winter moth embryonic development rate in response to temperature. Over the course of development, we sampled eggs before and after an experimental change in ambient temperature, including two early development weeks when the temperature sensitivity of eggs is low and two late development weeks when temperature sensitivity is high. We found temperature-responsive genes that responded in a similar way across development, as well as genes with a temperature response specific to a particular development week. Moreover, we identified genes whose temperature effect size changed around the switch in temperature sensitivity of development rate. Interesting candidate genes for regulating the temperature sensitivity of egg development rate included genes involved in histone modification, hormonal signalling, nervous system development and circadian clock genes. The diverse sets of temperature-responsive genes we found here indicate that there are many potential targets of selection to change the temperature sensitivity of embryonic development rate. Identifying for which of these genes there is genetic variation in wild insect populations will give insight into their adaptive potential in the face of climate change.

A chromosome-level genome of Semiothisa cinerearia provides insights into its genome evolution and control

BACKGROUND

Semiothisa cinerearia belongs to Geometridae, which is one of the most species-rich families of lepidopteran insects. It is also one of the most economically significant pests of the Chinese scholar tree (Sophora japonica L.), which is an important urban greenbelt trees in China due to its high ornamental value. A genome assembly of S. cinerearia would facilitate study of the control and evolution of this species.

RESULTS

We present a reference genome for S. cinerearia; the size of the genome was ~ 580.89 Mb, and it contained 31 chromosomes. Approximately 43.52% of the sequences in the genome were repeat sequences, and 21,377 protein-coding genes were predicted. Some important gene families involved in the detoxification of pesticides (P450) have expanded in S. cinerearia. Cytochrome P450 gene family members play key roles in mediating relationships between plants and insects, and they are important in plant secondary metabolite detoxification and host-plant selection. Using comparative analysis methods, we find positively selected gene, Sox15 and TipE, which may play important roles during the larval-pupal metamorphosis development of S. cinerearia.

CONCLUSION

This assembly provides a new genomic resource that will aid future comparative genomic studies of Geometridae species and facilitate future evolutionary studies on the S. cinerearia.

One's trash is someone else's treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts

BACKGROUND

Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts' life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis.

RESULTS

In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here.

CONCLUSIONS

Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.

Chromosomal-level reference genome of the moth Heortia vitessoides (Lepidoptera: Crambidae), a major pest of agarwood-producing trees

The moth Heortia vitessoides Moore (Lepidoptera: Crambidae) is a major pest of ecologically, commercially and culturally important agarwood-producing trees in the genus Aquilaria. In particular, H. vitessoides is one of the most destructive defoliating pests of the incense tree Aquilaria sinesis, which produces a valuable fragrant wood used as incense and in traditional Chinese medicine [33]. Nevertheless, a genomic resource for H. vitessoides is lacking. Here, we present a chromosomal-level assembly for H. vitessoides, consisting of a 517 megabase (Mb) genome assembly with high physical contiguity (scaffold N50 of 18.2 Mb) and high completeness (97.9% complete BUSCO score). To aid gene annotation, 8 messenger RNA transcriptomes from different developmental stages were generated, and a total of 16,421 gene models were predicted. Expansion of gene families involved in xenobiotic metabolism and development were detected, including duplications of cytosolic sulfotransferase (SULT) genes shared among lepidopterans. In addition, small RNA sequencing of 5 developmental stages of H. vitessoides facilitated the identification of 85 lepidopteran conserved microRNAs, 94 lineage-specific microRNAs, as well as several microRNA clusters. A large proportion of the H. vitessoides genome consists of repeats, with a 29.12% total genomic contribution from transposable elements, of which long interspersed nuclear elements (LINEs) are the dominant component (17.41%). A sharp decrease in the genome-wide percentage of LINEs with lower levels of genetic distance to family consensus sequences suggests that LINE activity has peaked in H. vitessoides. In contrast, opposing patterns suggest a substantial recent increase in DNA and LTR element activity. Together with annotations of essential sesquiterpenoid hormonal pathways, neuropeptides, microRNAs and transposable elements, the high-quality genomic and transcriptomic resources we provide for the economically important moth H. vitessoides provide a platform for the development of genomic approaches to pest management, and contribute to addressing fundamental research questions in Lepidoptera.

Molecular Oscillator Affects Susceptibility of Caterpillars to Insecticides: Studies on the Egyptian Cotton Leaf Worm-Spodoptera littoralis (Lepidoptera: Noctuidae)

The molecular oscillator is the core of the biological clock and is formed by genes and proteins whose cyclic expression is regulated in the transcriptional-translational feedback loops (TTFLs). Proteins of the TTFLs are regulators of both their own and executive genes involved in the control of many processes in insects (e.g., rhythmic metabolism of xenobiotics, including insecticides). We disrupted the clock operation in S. littoralis larvae by injecting the dsRNA of clock genes into their body cavity and culturing the larvae under continuous light. As a result, the daily susceptibility of larvae to insecticides was abolished and the susceptibility itself increased (in most cases). In the fat body, midgut, and Malpighian tubules (the main organs metabolizing xenobiotics) of the larvae treated with injected-dsRNA, the daily activity profiles of enzymes involved in detoxification-cytochrome P450 monooxygenases, Glutathione-S-transferase, and esterase-have changed significantly. The presented results prove the role of the molecular oscillator in the regulation of larvae responses to insecticides and provide grounds for rational use of these compounds (at suitable times of the day), and may indicate clock genes as potential targets of molecular manipulation to produce plant protection compounds based on the RNAi method.

The Circadian Clock in Lepidoptera

With approximately 160,000 identified species of butterflies and moths, Lepidoptera are among the most species-rich and diverse insect orders. Lepidopteran insects have fundamental ecosystem functions as pollinators and valuable food sources for countless animals. Furthermore, Lepidoptera have a significant impact on the economy and global food security because many species in their larval stage are harmful pests of staple food crops. Moreover, domesticated species such as the silkworm Bombyx mori produce silk and silk byproducts that are utilized by the luxury textile, biomedical, and cosmetics sectors. Several Lepidoptera have been fundamental as model organisms for basic biological research, from formal genetics to evolutionary studies. Regarding chronobiology, in the 1970s, Truman's seminal transplantation experiments on different lepidopteran species were the first to show that the circadian clock resides in the brain. With the implementation of molecular genetics, subsequent studies identified key differences in core components of the molecular circadian clock of Lepidoptera compared to the dipteran Drosophila melanogaster, the dominant insect species in chronobiological research. More recently, studies on the butterfly Danaus plexippus have been fundamental in characterizing the interplay between the circadian clock and navigation during the seasonal migration of this species. Moreover, the advent of Next Generation Omic technologies has resulted in the production of many publicly available datasets regarding circadian clocks in pest and beneficial Lepidoptera. This review presents an updated overview of the molecular and anatomical organization of the circadian clock in Lepidoptera. We report different behavioral circadian rhythms currently identified, focusing on the importance of the circadian clock in controlling developmental, mating and migration phenotypes. We then describe the ecological importance of circadian clocks detailing the complex interplay between the feeding behavior of these organisms and plants. Finally, we discuss how the characterization of these features could be useful in both pest control, and in optimizing rearing of beneficial Lepidoptera.

Nine Mitochondrial Genomes of the Pyraloidea and Their Phylogenetic Implications (Lepidoptera)

Simple Summary

The Pyraloidea is a large superfamily of Lepidoptera in species composition. To date, the higher-level phylogenetic relationships in this group remain unresolved, and many taxa, with taxonomic positions historically established by morphological characters, need to be confirmed through sequencing of DNA, including mitochondrial genome sequences (mitogenomes). Here, we newly generated nine complete mitogenomes for Pyraloidea that shared identical gene content, and arrangements that are typical of Lepidoptera. The current phylogenetic results confirmed previous multilocus studies, indicating the effectiveness of mitogenomes for inference of Pyraloidea higher-level relationships. Unexpectedly, Orybina Snellen was robustly placed as basal to the remaining Pyralidae taxa, rather than nested in the Pyralinae of Pyralidae as morphologically defined and placed. Our results bring a greater understanding to Pyraloidea phylogeny, and highlight the necessity of sequencing more pyraloid taxa to reevaluate their phylogenetic positions.

Abstract

The Pyraloidea is one of the species-rich superfamilies of Lepidoptera and contains numerous economically important pest species that cause great loss in crop production. Here, we sequenced and annotated nine complete mitogenomes for Pyraloidea, and further performed various phylogenetic analyses, to improve our understanding of mitogenomic evolution and phylogeny of this superfamily. The nine mitogenomes were circular, double-stranded molecules, with the lengths ranging from 15,214 bp to 15,422 bp, which are comparable to other reported pyraloid mitogenomes in size. Gene content and arrangement were highly conserved and are typical of Lepidoptera. Based on the hitherto most extensive mitogenomic sampling, our various resulting trees showed generally congruent topologies among pyraloid subfamilies, which are almost in accordance with previous multilocus studies, indicating the suitability of mitogenomes in inferring high-level relationships of Pyraloidea. However, nodes linking subfamilies in the “non-PS clade” were not completely resolved in terms of unstable topologies or low supports, and future investigations are needed with increased taxon sampling and molecular data. Unexpectedly, Orybina Snellen, represented in a molecular phylogenetic investigation for the first time, was robustly placed as basal to the remaining Pyralidae taxa across our analyses, rather than nested in Pyralinae of Pyralidae as morphologically defined. This novel finding highlights the need to reevaluate Orybina monophyly and its phylogenetic position by incorporating additional molecular and morphological evidence.

Four times out of Europe: Serial invasions of the winter moth, Operophtera brumata, to North America

Reconstructing the geographic origins of non-native species is important for studying the factors that influence invasion success, however; these analyses can be constrained by the amount of diversity present in the native and invaded regions, and by changes in the genetic background of the invading population following bottlenecks and/or hybridization events. Here we explore the geographical origins of the invasive winter moth (Operopthera brumata L.) that has caused widespread defoliation to forests, orchards, and crops in Nova Scotia, British Columbia, Oregon, and the northeastern United States. It is not known whether these represent independent introductions to North America, or a "stepping stone" spread among regions. Using a combination of Bayesian assignment and approximate Bayesian computation methods, we analysed a population genetic data set of 24 microsatellite loci. We estimate that winter moth was introduced to North America on at least four occasions, with the Nova Scotian and British Columbian populations probably being introduced from France and Sweden, respectively; the Oregonian population probably being introduced from either the British Isles or northern Fennoscandia; and the population in the northeastern United States probably being introduced from somewhere in Central Europe. We discuss the impact of genetic bottlenecks on analyses meant to determine region of origin.

Prevalence and relationship of endosymbiotic Wolbachia in the butterfly genus Erebia

BACKGROUND

Wolbachia is an endosymbiont common to most invertebrates, which can have significant evolutionary implications for its host species by acting as a barrier to gene flow. Despite the importance of Wolbachia, still little is known about its prevalence and diversification pattern among closely related host species. Wolbachia strains may phylogenetically coevolve with their hosts, unless horizontal host-switches are particularly common. We address  these issues in the genus Erebia, one of the most diverse Palearctic butterfly genera.

RESULTS

We sequenced the Wolbachia genome from a strain infecting Erebia cassioides and showed that it belongs to the Wolbachia supergroup B, capable of infecting arthropods from different taxonomic orders. The prevalence of Wolbachia across 13 closely related Erebia host species based on extensive population-level genetic data revealed that multiple Wolbachia strains jointly infect all investigated taxa, but with varying prevalence. Finally, the phylogenetic relationships of Wolbachia strains are in some cases significantly associated to that of their hosts, especially among the most closely related Erebia species, demonstrating mixed evidence for phylogenetic coevolution.

CONCLUSIONS

Closely related host species can be infected by closely related Wolbachia strains, evidencing some phylogenetic coevolution, but the actual pattern of infection more often reflects historical or contemporary geographic proximity among host species. Multiple processes, including survival in distinct glacial refugia, recent host shifts in sympatry, and a loss of Wolbachia during postglacial range expansion seem to have jointly shaped the complex interactions between Wolbachia evolution and the diversification of its host among our studied Erebia species.

Involvement of Methoprene-tolerant and Krüppel homolog 1 in juvenile hormone-signaling regulating the maturation of male accessory glands in the moth Agrotis ipsilon

Male accessory glands (MAGs) produce seminal fluid proteins that are essential for the fertility and also influence the reproductive physiology and behavior of mated females. In many insect species, and especially in the moth Agrotis ipsilon, juvenile hormone (JH) promotes the maturation of the MAGs but the underlying molecular mechanisms in this hormonal regulation are not yet well identified. Here, we examined the role of the JH receptor, Methoprene-tolerant (Met) and the JH-inducible transcription factor, Krüppel homolog 1 (Kr-h1) in transmitting the JH signal that upregulates the growth and synthetic activity of the MAGs in A. ipsilon. We cloned two full length cDNAs encoding Met1 and Met2 which are co-expressed with Kr-h1 in the MAGs where their expression levels increase with age in parallel with the length and protein content of the MAGs. RNAi-mediated knockdown of either Met1, Met2, or Kr-h1 resulted in reduced MAG length and protein amount. Moreover, injection of JH-II into newly emerged adult males induced the transcription of Met1, Met2 and Kr-h1 associated to an increase in the length and protein content of the MAGs. By contrast, JH deficiency decreased Met1, Met2 and Kr-h1 mRNA levels as well as the length and protein reserves of the MAGs of allatectomized old males and these declines were partly compensated by a combined injection of JH-II in operated males. Taken together, our results highlighted an involvement of the JH-Met-Kr-h1 signaling pathway in the development and secretory activity of the MAGs in A. ipsilon.

Chromosome-level genome reference and genome editing of the tea geometrid

The tea geometrid is a destructive insect pest on tea plants, which seriously affects tea production in terms of both yield and quality and causes severe economic losses. The tea geometrid also provides an important study system to address the ecological adaptive mechanisms underlying its unique host plant adaptation and protective resemblance. In this study, we fully sequenced and de novo assembled the reference genome of the tea geometrid, Ectropis grisescens, using long sequencing reads. We presented a highly continuous, near-complete genome reference (787.4 Mb; scaffold N50: 26.9 Mb), along with the annotation of 18,746 protein-coding genes and 53.3% repeat contents. Importantly, we successfully placed 97.8% of the assembly in 31 chromosomes based on Hi-C interactions and characterized the sex chromosome based on sex-biased sequencing coverage. Multiple quality-control assays and chromosome-scale synteny with the model species all supported the high quality of the presented genome reference. We focused biological annotations on gene families related to the host plant adaptation and camouflage in the tea geometrid and performed comparisons with other representative lepidopteran species. Important findings include the E. grisescens-specific expansion of CYP6 P450 genes that might be involved in metabolism of tea defensive chemicals and unexpected massive expansion of gustatory receptor gene families that suggests potential polyphagy for this tea pest. Furthermore, we developed an efficient genome editing system based on CRISPR/Cas9 technology and successfully implement mutagenesis of a Hox gene in the tea geometrid. Our study provides key genomic resources both for exploring unique mechanisms underlying the ecological adaptation of tea geometrids and for developing environment-friendly strategies for tea pest management.

Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

While two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome analysed. Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a tenfold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of this genus representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicates that while large genomes evolved by an accumulation of retrotransposons, the smallest genome known for the genus has evolved by diversification of different repeat types, particularly satDNAs.

The Wolbachia Symbiont: Here, There and Everywhere

Wolbachia symbionts, first observed in the 1920s, are now known to be present in about 30-70% of tested arthropod species, in about half of tested filarial nematodes (including the majority of human filarial nematodes), and some plant-parasitic nematodes. In arthropods, they are generally viewed as parasites while in nematodes they appear to be mutualists although this demarcation is not absolute. Their presence in arthropods generally leads to reproductive anomalies, while in nematodes, they are generally required for worm development and reproduction. In mosquitos, Wolbachia inhibit RNA viral infections, leading to populational reductions in human RNA virus pathogens, whereas in filarial nematodes, their requirement for worm fertility and survival has been channeled into their use as drug targets for filariasis control. While much more research on these ubiquitous symbionts is needed, they are viewed as playing significant roles in biological processes, ranging from arthropod speciation to human health.

Ecdysis triggering hormone modulates molt behaviour in the redclaw crayfish Cherax quadricarinatus, providing a mechanistic evidence for conserved function in molt regulation across Pancrustacea

Molting enables growth and development across ecdysozoa. The molting process is strictly controlled by hormones - ecdysteroids. Ecdysteroidogenesis occurs in theprothoracic glands and stimulated by prothoracicotropic hormone in insects, while it ensues in the Y-organ and regulated by the molt inhibiting hormone in crustaceans. A peak in ecdysteroids in the hemolymph induces a cascade of multiple neuropeptides including Ecdysis Triggering Hormone (ETH) and Corazonin. The role of ETH is well defined in controlling the molt process in insects, but it is yet to be defined in crustaceans. In this study, we investigated the behavioral response of intermolt crayfish to ETH and Corazonin injections as well as the impact of ETH on the molt period using in vivo assays. Injection of Corazonin and ETH resulted in a clear and immediate eye twitching response to these two neuropeptides. The Corazonin injection induced eye twitching in slow and asynchronous manner, while ETH injection caused eye twitching in a relatively fast and synchronous way. A single injection of ETH to crayfish resulted in a remarkable prolong molt period, at twice the normal molting cycle, suggesting that ETH plays a key role in controlling the molt cycle in decapod crustaceans. Given the key significance of ETH in molt regulation and its plausible application in pest control, we characterized ETH across the pancrustacean orders. Bioinformatic analysis shows the mature ETH sequence is identical in all studied decapod species. ETH can be classified into specific groups based on the associated motif in each insect order and shows an insect motif -KxxPRx to be conserved in crustaceans.

Involvement of Two Paralogous Methoprene-Tolerant Genes in the Regulation of Vitellogenin and Vitellogenin Receptor Expression in the Rice Stem Borer, Chilo suppressalis

Besides the function of preventing metamorphosis in insects, the juvenile hormone (JH) plays a role in female reproduction; however, the underlying mechanism is largely unknown. The methoprene-tolerant (Met) protein belongs to a family of basic helix-loop-helix–Per-Arnt-Sim (bHLH-PAS) transcription factors and functions as the JH intracellular receptor. In this study, two full length cDNAs encoding Met (CsMet1 and CsMet2) were isolated from the rice stem borer, Chilo suppressalis. Structural analysis revealed that both CsMet1 and CsMet2 exhibited typical bHLH, PAS-A, PAS-B, and PAC (PAS C terminal motif) domains. Comparative analysis of transcript level using reverse transcription-quantitative PCR (RT-qPCR) revealed that CsMet1 was predominant in almost all examined developmental stages and tissues. Treatment with methoprene in vivo induces the transcription of both CsMet1 and CsMet2. Notably, injection of dsCsMet1 and dsCsMet2 suppressed the expression levels of vitellogenin (CsVg) and Vg receptor (CsVgR). These findings revealed the potential JH signaling mechanism regulating C. suppressalis reproduction, and provided evidence that RNAi-mediated knockdown of Met holds great potential as a control strategy of C. suppressalis.

Molecular cloning and comparative analysis of transcripts encoding chemosensory proteins from two plant bugs, Lygus lineolaris and Lygus hesperus

Chemosensory proteins (CSPs) are soluble carrier proteins typically characterized by a six-helix bundle structure joined by two disulfide bridges and a conserved Cys spacing pattern (C1-X_6-8 -C2-X_16-21 -C3-X₂ -C4). CSPs are functionally diverse with reported roles in chemosensation, immunity, development, and resistance. To expand our molecular understanding of CSP function in plant bugs, we used recently developed transcriptomic resources for Lygus lineolaris and Lygus hesperus to identify 17 and 14 CSP-like sequences, respectively. The Lygus CSPs are orthologous and share significant sequence identity with previously annotated CSPs. Three of the CSPs are predicted to deviate from the typical CSP structure with either five or seven helical segments rather than six. The seven helix CSP is further differentiated by an atypical C3-X₃ -C4 Cys spacing motif. Reverse transcriptase PCR-based profiling of CSP transcript abundance in adult L. lineolaris tissues revealed broad expression for most of the CSPs with antenna specific expression limited to a subset of the CSPs. Comparative sequence analyses and homology modeling suggest that variations in the amino acids that comprise the Lygus CSP binding pockets affect the size and nature of the ligands accommodated.

Genome of the webworm Hyphantria cunea unveils genetic adaptations supporting its rapid invasion and spread

BACKGROUND

The fall webworm Hyphantria cunea is an invasive and polyphagous defoliator pest that feeds on nearly any type of deciduous tree worldwide. The silk web of H. cunea aids its aggregating behavior, provides thermal regulation and is regarded as one of causes for its rapid spread. In addition, both chemosensory and detoxification genes are vital for host adaptation in insects.

RESULTS

Here, a high-quality genome of H. cunea was obtained. Silk-web-related genes were identified from the genome, and successful silencing of the silk protein gene HcunFib-H resulted in a significant decrease in silk web shelter production. The CAFE analysis showed that some chemosensory and detoxification gene families, such as CSPs, CCEs, GSTs and UGTs, were expanded. A transcriptome analysis using the newly sequenced H. cunea genome showed that most chemosensory genes were specifically expressed in the antennae, while most detoxification genes were highly expressed during the feeding peak. Moreover, we found that many nutrient-related genes and one detoxification gene, HcunP450 (CYP306A1), were under significant positive selection, suggesting a crucial role of these genes in host adaptation in H. cunea. At the metagenomic level, several microbial communities in H. cunea gut and their metabolic pathways might be beneficial to H. cunea for nutrient metabolism and detoxification, and might also contribute to its host adaptation.

CONCLUSIONS

These findings explain the host and environmental adaptations of H. cunea at the genetic level and provide partial evidence for the cause of its rapid invasion and potential gene targets for innovative pest management strategies.

Identification of winter moth (Operophtera brumata) refugia in North Africa and the Italian Peninsula during the last glacial maximum

Numerous studies have shown that the genetic diversity of species inhabiting temperate regions has been shaped by changes in their distributions during the Quaternary climatic oscillations. For some species, the genetic distinctness of isolated populations is maintained during secondary contact, while for others, admixture is frequently observed. For the winter moth (Operophtera brumata), an important defoliator of oak forests across Europe and northern Africa, we previously determined that contemporary populations correspond to genetic diversity obtained during the last glacial maximum (LGM) through the use of refugia in the Iberian and Aegean peninsulas, and to a lesser extent the Caucasus region. Missing from this sampling were populations from the Italian peninsula and from North Africa, both regions known to have played important roles as glacial refugia for other species. Therefore, we genotyped field-collected winter moth individuals from southern Italy and northwestern Tunisia-the latter a region where severe oak forest defoliation by winter moth has recently been reported-using polymorphic microsatellite. We reconstructed the genetic relationships of these populations in comparison to moths previously sampled from the Iberian and Aegean peninsulas, the Caucasus region, and western Europe using genetic distance, Bayesian clustering, and approximate Bayesian computation (ABC) methods. Our results indicate that both the southern Italian and the Tunisian populations are genetically distinct from other sampled populations, and likely originated in their respective refugium during the LGM after diverging from a population that eventually settled in the Iberian refugium. These suggest that winter moth populations persisted in at least five Mediterranean LGM refugia. Finally, we comment that outbreaks by winter moth in northwestern Tunisia are not the result of a recent introduction of a nonnative species, but rather are most likely due to land use or environmental changes.

Complete mitochondrial genome of Acropteris iphiata (Lepidoptera: Uraniidae)

Acropteris iphiata belongs to the family Uraniidae in the superfamily Geometroidea (Lepidoptera). We sequenced 15,346-bp long complete mitochondrial genome (mitogenome) of the species, which consists of a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one major non-coding A + T-rich region. The A. iphiata mitogenome harbored the gene order tRNA^Met, tRNA^Ile, and tRNA^Gln between the A + T-rich region and ND2 that is found in most lepidopteran mitogenomes. Bayesian inference (BI) and maximum likelihood (ML) phylogeny, using 13 protein-coding genes (PCGs) and 2 rRNAs showed that A. iphiata was placed as a sister to Geometridae with the highest nodal support (Bayesian posterior probabilities for BI = 1.00 and Bootstrap support for ML = 100).

The bagworm genome reveals a unique fibroin gene that provides high tensile strength

Arthropod silk is known as a versatile tool, and its variability makes it an attractive biomaterial. Eumeta variegata is a bagworm moth (Lepidoptera, Psychidae) that uses silk throughout all life stages. Notably, the bagworm-specific uses of silk include larval development in a bag coated with silk and plant materials and the use of silk attachments to hang pupae. An understanding at the molecular level of bagworm silk, which enables such unique purposes, is an opportunity to expand the possibilities for artificial biomaterial design. However, very little is known about the bagworm fibroin gene and the mechanical properties of bagworm silk. Here, we report the bagworm genome, including a silk fibroin gene. The genome is approximately 700 Mbp in size, and the newly found fibroin gene has a unique repetitive motif. Furthermore, a mechanical property test demonstrates a phylogenetic relationship between the unique motif and tensile strength of bagworm silk.

Gypsy moth genome provides insights into flight capability and virus-host interactions

Since its accidental introduction to Massachusetts in the late 1800s, the European gypsy moth (EGM; Lymantria dispar dispar) has become a major defoliator in North American forests. However, in part because females are flightless, the spread of the EGM across the United States and Canada has been relatively slow over the past 150 years. In contrast, females of the Asian gypsy moth (AGM; Lymantria dispar asiatica) subspecies have fully developed wings and can fly, thereby posing a serious economic threat if populations are established in North America. To explore the genetic determinants of these phenotypic differences, we sequenced and annotated a draft genome of L. dispar and used it to identify genetic variation between EGM and AGM populations. The 865-Mb gypsy moth genome is the largest Lepidoptera genome sequenced to date and encodes ∼13,300 proteins. Gene ontology analyses of EGM and AGM samples revealed divergence between these populations in genes enriched for several gene ontology categories related to muscle adaptation, chemosensory communication, detoxification of food plant foliage, and immunity. These genetic differences likely contribute to variations in flight ability, chemical sensing, and pathogen interactions among EGM and AGM populations. Finally, we use our new genomic and transcriptomic tools to provide insights into genome-wide gene-expression changes of the gypsy moth after viral infection. Characterizing the immunological response of gypsy moths to virus infection may aid in the improvement of virus-based bioinsecticides currently used to control larval populations.

Selection at a genomic region of major effect is responsible for evolution of complex life histories in anadromous steelhead

BACKGROUND

Disparity in the timing of biological events occurs across a variety of systems, yet the understanding of genetic basis underlying diverse phenologies remains limited. Variation in maturation timing occurs in steelhead trout, which has been associated with greb1L, an oestrogen target gene. Previous techniques that identified this gene only accounted for about 0.5-2.0% of the genome and solely investigated coastal populations, leaving uncertainty on the genetic basis of this trait and its prevalence across a larger geographic scale.

RESULTS

We used a three-tiered approach to interrogate the genomic basis of complex phenology in anadromous steelhead. First, fine scale mapping with 5.3 million SNPs from resequencing data covering 68% of the genome confirmed a 309-kb region consisting of four genes on chromosome 28, including greb1L, to be the genomic region of major effect for maturation timing. Second, broad-scale characterization of candidate greb1L genotypes across 59 populations revealed unexpected patterns in maturation phenology for inland fish migrating long distances relative to those in coastal streams. Finally, genotypes from 890 PIT-tag tracked steelhead determined associations with early versus late arrival to spawning grounds that were previously unknown.

CONCLUSIONS

This study clarifies the genetic bases for disparity in phenology observed in steelhead, determining an unanticipated trait association with premature versus mature arrival to spawning grounds and identifying multiple candidate genes potentially contributing to this variation from a single genomic region of major effect. This illustrates how dense genome mapping and detailed phenotypic characterization can clarify genotype to phenotype associations across geographic ranges of species.

A bioinformatics approach to identifying Wolbachia infections in arthropods

Wolbachia is the most widespread endosymbiont, infecting >20% of arthropod species, and capable of drastically manipulating the host's reproductive mechanisms. Conventionally, diagnosis has relied on PCR amplification; however, PCR is not always a reliable diagnostic technique due to primer specificity, strain diversity, degree of infection and/or tissue sampled. Here, we look for evidence of Wolbachia infection across a wide array of arthropod species using a bioinformatic approach to detect the Wolbachia genes ftsZ, wsp, and the groE operon in next-generation sequencing samples available through the NCBI Sequence Read Archive. For samples showing signs of infection, we attempted to assemble entire Wolbachia genomes, and in order to better understand the relationships between hosts and symbionts, phylogenies were constructed using the assembled gene sequences. Out of the 34 species with positively identified infections, eight species of arthropod had not previously been recorded to harbor Wolbachia infection. All putative infections cluster with known representative strains belonging to supergroup A or B, which are known to only infect arthropods. This study presents an efficient bioinformatic approach for post-sequencing diagnosis and analysis of Wolbachia infection in arthropods.

Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts

The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host’s body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse. Furthermore, heritable endosymbionts have been repeatedly demonstrated to play an integral role in many aspects of host biology, particularly host reproduction. Here, we review the major findings of research of heritable microbial endosymbionts of butterflies and moths. We promote the Lepidoptera as important models in the study of reproductive manipulations employed by heritable endosymbionts, with the mechanisms underlying male-killing and feminisation currently being elucidated in moths and butterflies. We also reveal that the vast majority of research undertaken of Lepidopteran endosymbionts concerns Wolbachia. While this highly prevalent bacterium is undoubtedly important, studies should move towards investigating the presence of other, and interacting endosymbionts, and we discuss the merits of examining the microbiome of Lepidoptera to this end. We finally consider the importance of understanding the influence of endosymbionts under global environmental change and when planning conservation management of endangered Lepidoptera species.

Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Background

The European spurge hawkmoth, Hyles euphorbiae (Lepidoptera, Sphingidae), has been intensively studied as a model organism for insect chemical ecology, cold hardiness and evolution of species delineation. To understand species isolation mechanisms at a molecular level, this study aims at determining genetic factors underlying two adaptive ecological trait candidates, phorbol ester (TPA) detoxification and seasonal cold acclimation.

Method

A draft transcriptome of H. euphorbiae was generated using Illumina sequencing, providing the first genomic resource for the hawkmoth subfamily Macroglossinae. RNA expression levels in tissues of experimental TPA feeding larvae and cooled pupae was compared to levels in control larvae and pupae using 26 bp RNA sequence tag libraries (DeepSuperSAGE). Differential gene expression was assessed by homology searches of the tags in the transcriptome.

Results

In total, 389 and 605 differentially expressed transcripts for detoxification and cold hardiness, respectively, could be identified and annotated with proteins. The majority (22 of 28) of differentially expressed detox transcripts of the four 'drug metabolism' enzyme groups (cytochrome P450 (CYP), carboxylesterases (CES), glutathione S-transferases (GST) and lipases) are up-regulated. Triacylglycerol lipase was significantly over proportionally annotated among up-regulated detox transcripts. We record several up-regulated lipases, GSTe2, two CESs, CYP9A21, CYP6BD6 and CYP9A17 as candidate genes for further H. euphorbiae TPA detoxification analyses. Differential gene expression of the cold acclimation treatment is marked by metabolic depression with enriched Gene Ontology terms among down-regulated transcripts almost exclusively comprising metabolism, aerobic respiration and dissimilative functions. Down-regulated transcripts include energy expensive respiratory proteins like NADH dehydrogenase, cytochrome oxidase and ATP synthase. Gene expression patterns show shifts in carbohydrate metabolism towards cryoprotectant production. The Glycolysis enzymes, G1Pase, A1e, Gpi and an Akr isoform are up-regulated. Glycerol, an osmolyte which lowers the body liquid supercooling point, appears to be the predominant polyol cryoprotectant in H. euphorbiae diapause pupae. Several protein candidates involved in glucose, glycerol, myo-inositol and potentially sorbitol and trehalose synthesis were identified.

Conclusions

A majority of differently expressed transcripts unique for either detoxification or cold hardiness indicates highly specialized functional adaptation which may have evolved from general cell metabolism and stress response.The transcriptome and extracted candidate biomarkers provide a basis for further gene expression studies of physiological processes and adaptive traits in H. euphorbiae.

Phylogeny and evolution of the cholesterol transporter NPC1 in insects

Sterols are essential nutrients for eukaryotes. Insects are obligate sterol auxotrophs and must acquire this key nutrient from their diets. The digestive tract is the organ for absorbing nutrients as well as sterols from food. In mice, the Niemann-Pick type C1 Like 1 (NPC1L1) gene is highly expressed in the intestine and is critical for cholesterol absorption. In contrast, the molecular mechanisms for the absorption of dietary sterols in insects have not been well studied. We annotated NPC1 genes in 39 insects from 10 orders using available genomic and transcriptomic information and inferred phylogenetic relationships. Insect NPC1 genes were grouped into two sister-clades, NPC1a and NPC1b, suggesting a likely duplication in the ancestor of insects. The former exhibited weaker gut-biased expression or a complete lack of tissue-biased expression, depending on the species, while the latter was highly enriched in the gut of three lepidopteran species. This result is similar to previous findings in Drosophila melanogaster. In insects, NPC1a accumulated non-synonymous substitutions at a lower rate than NPC1b. This pattern was consistent across orders, indicating that NPC1a evolved under stronger molecular constraint than NPC1b.

Gene Identification of Pheromone Gland Genes Involved in Type II Sex Pheromone Biosynthesis and Transportation in Female Tea Pest Ectropis grisescens

Moths can biosynthesize sex pheromones in the female sex pheromone glands (PGs) and can distinguish species-specific sex pheromones using their antennae. However, the biosynthesis and transportation mechanism for Type II sex pheromone components has rarely been documented in moths. In this study, we constructed a massive PG transcriptome database (14.72 Gb) from a moth species, Ectropis grisescens, which uses type II sex pheromones and is a major tea pest in China. We further identified putative sex pheromone biosynthesis and transportation-related unigenes: 111 cytochrome P450 monooxygenases (CYPs), 25 odorant-binding proteins (OBPs), and 20 chemosensory proteins (CSPs). Tissue expression and phylogenetic tree analyses showed that one CYP (EgriCYP341-fragment3), one OBP (EgriOBP4), and one CSP (EgriCSP10) gene displayed an enriched expression in the PGs, and that EgriOBP2, 3, and 25 are clustered in the moth pheromone-binding protein clade. We considered these our candidate genes. Our results yielded large-scale PG sequence information for further functional studies.

Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well-studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537 Mb total length was assembled into 68,292 scaffolds (N50 = 164 kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine-scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome-predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high-quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/).

Lepidoptera genomes: current knowledge, gaps and future directions

Butterflies and moths (Lepidoptera) are one of the most ecologically diverse and speciose insect orders. With recent advances in genomics, new Lepidoptera genomes are regularly being sequenced, and many of them are playing principal roles in genomics studies, particularly in the fields of phylo-genomics and functional genomics. Thus far, assembled genomes are only available for <10 of the 43 Lepidoptera superfamilies. Nearly all are model species, found in the speciose clade Ditrysia. Community support for Lepidoptera genomics is growing with successful management and dissemination of data and analytical tools in centralized databases. With genomic studies quickly becoming integrated with ecological and evolutionary research, the Lepidoptera community will unquestionably benefit from new high-quality reference genomes that are more evenly distributed throughout the order.

Wolbachia in the Genus Bicyclus: a Forgotten Player

Bicyclus butterflies are key species for studies of wing pattern development, phenotypic plasticity, speciation and the genetics of Lepidoptera. One of the key endosymbionts in butterflies, the alpha-Proteobacterium Wolbachia pipientis, is affecting many of these biological processes; however, Bicyclus butterflies have not been investigated systematically as hosts to Wolbachia. In this study, we screen for Wolbachia infection in several Bicyclus species from natural populations across Africa as well as two laboratory populations. Out of the 24 species tested, 19 were found to be infected, and no double infection was found, but both A- and B-supergroup strains colonise this butterfly group. We also show that many of the Wolbachia strains identified in Bicyclus butterflies belong to the ST19 clonal complex. We discuss the importance of our results in regard to routinely screening for Wolbachia when using Bicyclus butterflies as the study organism of research in eco-evolutionary biology.

Purification and biochemical characterization of a novel transglutaminase from Mythimna separata larvae (Noctuidae, Lepidoptera)

A novel transglutaminase (MsTGase) from Mythimna separata larvae was separated and purified; its biochemical property and enzymatic catalytic activities were investigated. MsTGase was obtained chromatographically by the precipitation of Sephadex G-100 gel and DEAE-Cellulose-52 ion-exchange column with 48-fold purification and a reproducible yield of approximately 12%. Molecular weight of the MsTGase was 63.5 KDa and its N-terminal amino acid sequence was GKIEEG-LVI. Michaelis constant of the MsTGase for the substrate N-CBZ-Gln-Gly was 12.83mM with a V_max of 7.99U/mL. Optimum conditions for MsTGase activity were at 42°C and pH7.5. The enzyme didn't possess metal ion at its catalytic active site; its activity could be significantly inhibited by Mg²⁺, but activated by Ca²⁺. Chlorpyrifos and spinosad showed a strong potential to increase MsTGase activity, supporting the view that MsTGase was a novel target. Moreover, the formation of intermolecular cross-links of casein and bovine serum albumin polymerized by MsTGase in the presence of DTT was observed. These findings pave the way for future studies on the physiological role of MsTGase and the potential impact of its regulation on MsTGase-associated pest management.

The Operophtera brumata Nucleopolyhedrovirus (OpbuNPV) Represents an Early, Divergent Lineage within Genus Alphabaculovirus

Operophtera brumata nucleopolyhedrovirus (OpbuNPV) infects the larvae of the winter moth, Operophtera brumata. As part of an effort to explore the pesticidal potential of OpbuNPV, an isolate of this virus from Massachusetts (USA)-OpbuNPV-MA-was characterized by electron microscopy of OpbuNPV occlusion bodies (OBs) and by sequencing of the viral genome. The OBs of OpbuNPV-MA consisted of irregular polyhedra and contained virions consisting of a single rod-shaped nucleocapsid within each envelope. Presumptive cypovirus OBs were also detected in sections of the OB preparation. The OpbuNPV-MA genome assembly yielded a circular contig of 119,054 bp and was found to contain little genetic variation, with most polymorphisms occurring at a frequency of < 6%. A total of 130 open reading frames (ORFs) were annotated, including the 38 core genes of Baculoviridae, along with five homologous repeat (hr) regions. The results of BLASTp and phylogenetic analysis with selected ORFs indicated that OpbuNPV-MA is not closely related to other alphabaculoviruses. Phylogenies based on concatenated core gene amino acid sequence alignments placed OpbuNPV-MA on a basal branch lying outside other alphabaculovirus clades. These results indicate that OpbuNPV-MA represents a divergent baculovirus lineage that appeared early during the diversification of genus Alphabaculovirus.

Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: Birth, death and adaptation

Across insect genomes, the size of the cytochrome P450 monooxygenase (CYP) gene superfamily varies widely. CYPome size variation has been attributed to reciprocal adaptive radiations in insect detoxification genes in response to plant biosynthetic gene radiations driven by co-evolution between herbivores and their chemically defended hostplants. Alternatively, variation in CYPome size may be due to random "birth-and-death" processes, whereby exponential increase via gene duplications is limited by random decay via gene death or transition via divergence. We examined CYPome diversification in the genomes of seven Lepidoptera species varying in host breadth from monophagous (Bombyx mori) to highly polyphagous (Amyelois transitella). CYPome size largely reflects the size of Clan 3, the clan associated with xenobiotic detoxification, and to some extent phylogenetic age. Consistently across genomes, families CYP6, CYP9 and CYP321 are most diverse and CYP6AB, CYP6AE, CYP6B, CYP9A and CYP9G are most diverse among subfamilies. Higher gene number in subfamilies is due to duplications occurring primarily after speciation and specialization ("P450 blooms"), and the genes are arranged in clusters, indicative of active duplicating loci. In the parsnip webworm, Depressaria pastinacella, gene expression levels in large subfamilies are high relative to smaller subfamilies. Functional and phylogenetic data suggest a correlation between highly dynamic loci (reflective of extensive gene duplication, functionalization and in some cases loss) and the ability of enzymes encoded by these genes to metabolize hostplant defences, consistent with an adaptive, nonrandom process driven by ecological interactions.

Complete mitochondrial genome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae): genomic comparisons among macroheteroceran superfamilies

The mitochondrial genome (mitogenome) characteristics of the monotypic Lasiocampoidea are largely unknown, because only limited number of mitogenomes is available from this superfamily. In this study, we sequenced the complete mitogenome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae) and compared it to those of Lasiocampoidea and macroheteroceran superfamilies (59 species in six superfamilies). The 15,570-bp K. undans genome had one additional trnR that was located between trnA and trnN loci and this feature was unique in Macroheterocera, including Lasiocampoidea. Considering that the two trnR copies are located in tandem with proper secondary structures and identical anticodons, a gene duplication event might be responsible for the presence of the two tRNAs. Nearly all macroheteroceran species, excluding Lasiocampoidea, have a spacer sequence (1-34 bp) at the trnS2 and ND1 junction, but most lasiocampid species, including K. undans, have an overlap at the trnS2 and ND1 junction, which represents a different genomic feature in Lasiocampoidea. Nevertheless, a TTAGTAT motif, which is typically detected in Macroheterocera at the trnS2 and ND1 junction, was also detected in all Lasiocampoidea. In summary, the general mitogenome characteristics of Lasiocampoidea did not differ greatly from the remaining macroheteroceran superfamilies, but it did exhibit some unique features.