Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata

The diapausing mosquito Culex pipiens exhibits reduced levels of H3K27me2 in the fat body

Culex pipiens, the northern house mosquito, is a major vector of West Nile virus. To survive the severe winter, adult mosquitoes enter a diapause programme. Extended lifespan and an increase in lipid storage are key indicators of diapause. Post-translational modifications to histone proteins impact the expression of genes and have been linked to the lifespan and energy utilisation of numerous insects. Here, we investigated the potential contribution of epigenetic alterations in initiating diapause in this mosquito species. Multiple sequence alignment of H3 sequences from other insect species demonstrates a high conservation of the H3 histone in Cx. pipiens throughout evolution. We then compared the levels of histone methylation in the ovaries and fat body tissues of diapausing and non-diapausing Cx. pipiens using western blots. Our data indicate that histone methylation levels in the ovaries of Cx. pipiens do not change during diapause. In contrast, H3K27me2 levels decrease more than twofold in the fat body of diapausing mosquitoes relative to non-diapausing counterparts. H3K27 methylation plays a crucial role in chromosome activation and inactivation during development in many insect species. This is predominantly governed by polycomb repressor complex 2. Intriguingly, a previous ChIP-seq study demonstrated that the transcription factor FOXO (Forkhead box O) targets the genes that comprise this complex. In addition, H3K27me2 exhibits dynamic abundance throughout the diapause programme in Cx. pipiens, suggesting its potential role in the initial activation of the diapause programme. This study expands our understanding of the relationship between alterations in epigenetic regulation and diapause.

Transcription profiling reveals tissue-specific metabolic pathways in the fat body and ovary of the diapausing mosquito Culex pipiens

The northern house mosquito, Culex pipiens, employs diapause as an essential survival strategy during winter, inducing important phenotypic changes such as enhanced stress tolerance, lipid accumulation, and extended longevity. During diapause, the cessation of reproductive development represents another distinctive phenotypic change, underlining the need for adjusted modulation of gene expressions within the ovary. Although considerable advancements in screening gene expression profiles in diapausing and non-diapausing mosquitoes, there remains a gap in tissue-specific transcriptomic profiling that could elucidate the complicated formation of diverse diapause features in Cx. pipiens. Here, we filled this gap by utilizing RNA sequencing, providing a detailed examination of gene expression patterns in the fat body and ovary during diapause compared to non-diapause conditions. Functional annotation of upregulated genes identified associations with carbohydrate metabolism, stress tolerance, immunity, and epigenetic regulation. The validation of candidate genes using quantitative real-time PCR verified the differentially expressed genes identified in diapausing mosquitoes. Our findings contribute novel insights into potential regulators during diapause in Cx. pipiens, thereby opening possible avenues for developing innovative vector control strategies.

Lysine Methylation and Histone Modifications during Cold Stress of Insects: Freeze-Tolerant Eurosta solidaginis and Freeze-Avoiding Epiblema scudderiana

Overwintering survival by insects, whether of the freeze-tolerant or freeze-avoiding types, is typically associated with a strong suppression of metabolic rate (e.g., entry into diapause) that involves the differential expression of many genes with regulation at the transcriptional, translational or post-translational levels. Epigenetic modifications have been suggested to play a vital role in regulating cold responses of insects. However, knowledge of the roles of epigenetic mechanisms in modulating gene expression for winter survival of the larvae of two goldenrod gall formers, the freeze-tolerant dipteran Eurosta solidaginis and the freeze-avoiding lepidopteran Epiblema scudderiana, remain unknown. The current study evaluates the role of cold-induced lysine methylation and histone modifications, with enzymes of lysine methylation (SETD8, SETD7, SUV39H1, SMYD2 and ASH2L), as well as relative levels of histone H3 acetylation (H3K9ac, H3K18ac, H3K27ac, H3K56ac) and methylation (H3K4me1, H3K9me3, H3K36me2) examined in two insects. Significant (p < 0.05) reductions were observed in most of the targets of histone methylation/acetylation for decreasing temperatures of Ep. scudderiana larvae, whereas selected histone methylation/acetylation targets were conversely elevated (p < 0.05) in E. solidaginis, particularly under conditions of 5 °C for 4 h. Histone H3 expression was found to be variable without statistical differences in larval goldenrod gall moths and gall flies. These results provide basic information on the patterns of epigenetic regulation involved in insect cold hardiness.

Characterization of pre-diapause phase in the northern Drosophila species D. ezoana

Drosophila ezoana is a virilis group Drosophila species inhabiting northern latitudes. The flies enter adult reproductive diapause to survive winter upon exposure to short photoperiod conditions (short-day) over several consecutive days. Insect pre-diapause phase - the duration between the beginning of exposure to short days and expression of diapause is thought to be comprised of two distinct phases - (a) photoperiodic time measurement that detects short-days, followed by (b) physiological events leading to the expression of diapause phenotype. A short-day dependent segment of the pre-diapause phase thus approximates the process of photoperiodic time measurement. Continuous darkness has been found to be a neutral condition with respect to diapause regulation in many insect species. The effect of variable number of short-days followed by continuous darkness on diapause incidence thus allows identification of short-day dependent segment of pre-diapause phase thereby mapping the process of photo-periodic time measurement. Although, few weeks of exposure to short-days in adult stage is known to be sufficient for the expression of diapause in D. ezoana, the number of short days required for the completion of photo-periodic time measurement has never been systematically analysed. Our experiments show that continuous darkness is a neutral condition for diapause regulation also in D. ezoana. We utilized the neutral nature of continuous darkness to map the process of photoperiodic time measurement in the D. ezoana strain 124OJ8 which showed that integration of short-day photic cues over the first 10 days of pre-diapause phase is essential for diapause induction.

Genetic constraints in genes exhibiting splicing plasticity in facultative diapause

Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.

RNA N6-methyladenosine of DHAPAT and PAP involves in regulation of diapause of Bombyx mori via the lipid metabolism pathway

Environment-induced epigenetics are involved in diapause regulation, but the molecular mechanism that epigenetically couples nutrient metabolism to diapause regulation remains unclear. In this study, we paid special attention to the significant differences in the level of N6-adenosine methylation (m6A) of dihydroxyacetone phosphate acyltransferase (DHAPAT) and phosphatidate phosphatase (PAP) genes in the lipid metabolism pathway of the bivoltine silkworm (Bombyx mori) strain Qiufeng developed from eggs incubated at a normal temperature (QFHT, diapause egg producer) compared to those from eggs incubated at a low temperature (QFLT, non-diapause egg producer). We knocked down DHAPAT in the pupal stage of the QFLT group, resulting in the non-diapause destined eggs becoming diapausing eggs. In the PAP knockdown group, the colour of the non-diapause destined eggs changed from light yellow to pink 3 days after oviposition, but they hatched as normal. Moreover, we validated that YTHDF3 binds to m6A-modified DHAPAT and PAP mRNAs to promote their stability and translation. These results suggest that RNA m6A methylation participates in the diapause regulation of silkworm by changing the expression levels of DHAPAT and PAP and reveal that m6A epigenetic modification can be combined with a lipid metabolism signal pathway to participate in the regulation of insect diapause traits, which provides a clearer image for exploring the physiological basis of insect diapause.

Quantitative transcriptomic and proteomic analyses reveal the potential maintenance mechanism of female adult reproductive diapause in Chrysoperla nipponensis

BACKGROUND

The green lacewing Chrysoperla nipponensis is an important natural enemy of many insect pests and exhibits reproductive diapause to overwinter. Our previous studies showed that adult C. nipponensis enters reproductive diapause under a short-day photoperiod. However, the molecular mechanism underlying diapause maintenance in C. nipponensis is still unknown.

RESULTS

The total lipid and triglyceride content showed the reservation and degradation of energy during diapause in C. nipponensis. Thus, we performed combined transcriptomic and proteomic analyses of female reproductive diapause in C. nipponensis at three ecophysiological phases (initiation, maintenance and termination). A total of 64 388 unigenes and 5532 proteins were identified from the transcriptome and proteome. In-depth dissection of the gene-expression dynamics revealed that differentially expressed genes and proteins were predominately involved in the lipid and carbohydrate metabolic pathways, in particular fatty acid metabolism, metabolic pathways and the citrate cycle. Among of these genes, TIM, CLK, JHAMT2, PMK, HMGS, HMGR, FKBP39, Kr-h1, Phm, ECR, IR1, ILP3, ILP4, mTOR, ACC, LSD1 and LSD2 were differentially expressed in diapause and non-diapause female adults of C. nipponensis. The expression patterns of these genes were consistent with the occurrence of vitellogenesis and expression of either Vg or VgR.

CONCLUSION

Our findings indicated that diapause adult C. nipponensis accumulate energy resources to overwinter. Transcriptomic and proteomic analyses suggested candidate key genes involved in the maintenance of C. nipponensis during adult reproductive diapause. Taken together, these results provide in-depth knowledge to understand the maintenance mechanism of C. nipponensis during adult reproductive diapause. © 2023 Society of Chemical Industry.

Diapause-Linked Gene Expression Pattern and Related Candidate Duplicated Genes of the Mountain Butterfly Parnassius glacialis (Lepidoptera: Papilionidae) Revealed by Comprehensive Transcriptome Profiling

The mountain butterfly Parnassius glacialis is a representative species of the genus Parnassius, which probably originated in the high-altitude Qinhai–Tibet Plateau in the Miocene and later dispersed eastward into relatively low-altitude regions of central to eastern China. However, little is known about the molecular mechanisms underlying the long-term evolutionary adaptation to heterogeneous environmental conditions of this butterfly species. In this study, we obtained the high-throughput RNA-Seq data from twenty-four adult individuals in eight localities, covering nearly all known distributional areas in China, and firstly identified the diapause-linked gene expression pattern that is likely to correlate with local adaptation in adult P. glacialis populations. Secondly, we found a series of pathways responsible for hormone biosynthesis, energy metabolism and immune defense that also exhibited unique enrichment patterns in each group that are probably related to habitat-specific adaptability. Furthermore, we also identified a suite of duplicated genes (including two transposable elements) that are mostly co-expressed to promote the plastic responses to different environmental conditions. Together, these findings can help us to better understand this species’ successful colonization to distinct geographic areas from the western to eastern areas of China, and also provide us with some insights into the evolution of diapause in mountain Parnassius butterfly species.

Molecular signatures of diapause in the Asian longhorned beetle: Gene expression

Most previous studies on gene expression during insect diapause do not address among-tissue variation in physiological processes. We measured transcriptomic changes during larval diapause in the Asian longhorned beetle, Anoplophora glabripennis (Coleoptera: Cerambycidae). We conducted RNA-seq on fat body, the supraesophageal ganglion, midgut, hindgut, and Malpighian tubules during pre-diapause, diapause maintenance, post-diapause quiescence, and post-diapause development. We observed a small, but consistent, proportion of genes within each gene expression profile that were shared among tissues, lending support for a core set of diapause-associated genes whose expression is tissue-independent. We evaluated the overarching hypotheses that diapause would be associated with cell cycle arrest, developmental arrest, and increased stress tolerance and found evidence of repressed TOR and insulin signaling, reduced cell cycle activity and increased capacity of stress response via heat shock protein expression and remodeling of the cytoskeleton. However, these processes varied among tissues, with the brain and fat body appearing to maintain higher levels of cellular activity during diapause than the midgut or Malpighian tubules. We also observed temperature-dependent changes in gene expression during diapause maintenance, particularly in genes related to the heat shock response and MAPK, insulin, and TOR signaling pathways. Additionally, we provide evidence for epigenetic reorganization during the diapause/post-diapause quiescence transition and expression of genes involved in post-translational modification, highlighting the need for investigations of the protein activity of these candidate genes and processes. We conclude that diapause development is coordinated via diverse tissue-specific gene expression profiles and that canonical diapause phenotypes vary among tissues.

Evolution of casein kinase 1 and functional analysis of new doubletime mutants in Drosophila

Circadian clocks are timing devices that rhythmically adjust organism's behavior, physiology, and metabolism to the 24-h day-night cycle. Eukaryotic circadian clocks rely on several interlocked transcription-translation feedback loops, where protein stability is the key part of the delay between transcription and the appearance of the mature proteins within the feedback loops. In bilaterian animals, including mammals and insects, the circadian clock depends on a homologous set of proteins. Despite mostly conserved clock components among the fruit fly Drosophila and mammals, several lineage-specific differences exist. Here we have systematically explored the evolution and sequence variability of insect DBT proteins and their vertebrate homologs casein kinase 1 delta (CKIδ) and epsilon (CKIε), dated the origin and separation of CKIδ from CKIε, and identified at least three additional independent duplications of the CKIδ/ε gene in Petromyzon, Danio, and Xenopus. We determined conserved regions in DBT specific to Diptera, and functionally tested a subset of those in D. melanogaster. Replacement of Lysine K224 with acidic residues strongly impacts the free-running period even in heterozygous flies, whereas homozygous mutants are not viable. K224D mutants have a temperature compensation defect with longer free-running periods at higher temperatures, which is exactly the opposite trend of what was reported for corresponding mammalian mutants. All DBTs of dipteran insects contain the NKRQK motif at positions 220-224. The occurrence of this motif perfectly correlates with the presence of BRIDE OF DOUBLETIME, BDBT, in Diptera. BDBT is a non-canonical FK506-binding protein that physically interacts with Drosophila DBT. The phylogeny of FK506-binding proteins suggests that BDBT is either absent or highly modified in non-dipteran insects. In addition to in silico analysis of DBT/CKIδ/ε evolution and diversity, we have identified four novel casein kinase 1 genes specific to the Drosophila genus.

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.

Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae

The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. An extraordinary diversity in life histories, feeding habits and morphology are a hallmark of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm placement of Cryptochetidae as sister taxon to a large clade containing both Drosophilidae and Braulidae-the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.

Impact of temperature on dengue and chikungunya transmission by the mosquito Aedes albopictus

The mosquito Aedes albopictus is an invasive species first detected in Europe in Albania in 1979, and now established in 28 European countries. Temperature is a limiting factor in mosquito activities and in the transmission of associated arboviruses namely chikungunya (CHIKV) and dengue (DENV). Since 2007, local transmissions of CHIKV and DENV have been reported in mainland Europe, mainly in South Europe. Thus, the critical question is how far north transmission could occur. In this context, the Albanian infestation by Ae. albopictus is of interest because the species is present up to 1200 m of altitude; this allows using altitude as a proxy for latitude. Here we show that Ae. albopictus can transmit CHIKV at 28 °C as well as 20 °C, however, the transmission of DENV is only observed at 28 °C. We conclude that if temperature is the key environmental factor limiting transmission, then transmission of CHIKV, but not DENV is feasible in much of Europe.

Sexual dimorphism of diapause regulation in the hemipteran bug Pyrrhocoris apterus

Diapause is one of the major strategies for insects to prepare for and survive harsh seasons. In females, the absence of juvenile hormone (JH) is a hallmark of adult reproductive diapause, a developmental arrest, which is much less characterized in males. Here we show that juvenile hormone III skipped bisepoxide (JHSB₃) titers in hemolymph remarkably differ between reproductive males and females of the linden bug Pyrrhocoris apterus, whereas no JH was detected in diapausing adults of both sexes. Like in females, ectopic application of JH mimic effectively terminated male diapause through the canonical JH receptor components, Methoprene-tolerant and Taiman. In contrast to females, long photoperiod induced reproduction even in males with silenced JH reception or in males with removed corpus allatum (CA), the JH-producing gland. JHSB₃ was detected in the accessory glands (MAG) of reproductive males, unexpectedly, even in males without CA. If there is a source of JHSB₃ outside CA or a long-term storage of JHSB₃ in MAGs remains to be elucidated. These sex-related idiosyncrasies are further manifested in different dynamics of diapause termination in P. apterus by low temperature. We would like to propose that this sexual dimorphism of diapause regulation might be explained by the different reproductive costs for each sex.

Cryoprotective Metabolites Are Sourced from Both External Diet and Internal Macromolecular Reserves during Metabolic Reprogramming for Freeze Tolerance in Drosophilid Fly, Chymomyza costata

Many cold-acclimated insects accumulate high concentrations of low molecular weight cryoprotectants (CPs) in order to tolerate low subzero temperatures or internal freezing. The sources from which carbon skeletons for CP biosynthesis are driven, and the metabolic reprogramming linked to cold acclimation, are not sufficiently understood. Here we aim to resolve the metabolism of putative CPs by mapping relative changes in concentration of 56 metabolites and expression of 95 relevant genes as larvae of the drosophilid fly, Chymomyza costata transition from a freeze sensitive to a freeze tolerant phenotype during gradual cold acclimation. We found that C. costata larvae may directly assimilate amino acids proline and glutamate from diet to acquire at least half of their large proline stocks (up to 55 µg per average 2 mg larva). Metabolic conversion of internal glutamine reserves that build up in early diapause may explain the second half of proline accumulation, while the metabolic conversion of ornithine and the degradation of larval collagens and other proteins might be two additional minor sources. Next, we confirm that glycogen reserves represent the major source of glucose units for trehalose synthesis and accumulation (up to 27 µg per larva), while the diet may serve as an additional source. Finally, we suggest that interconversions of phospholipids may release accumulated glycero-phosphocholine (GPC) and -ethanolamine (GPE). Choline is a source of accumulated methylamines: glycine-betaine and sarcosine. The sum of methylamines together with GPE and GPC represents approximately 2 µg per larva. In conclusion, we found that food ingestion may be an important source of carbon skeletons for direct assimilation of, and/or metabolic conversions to, CPs in a diapausing and cold-acclimated insect. So far, the cold-acclimation- linked accumulation of CPs in insects was considered to be sourced mainly from internal macromolecular reserves.

Life stage and the environment as effectors of transposable element activity in two bee species

Diapause is a complex physiological phenomenon that allows insects to weather stressful environmental conditions. The regulation of diapause is accordingly complex, including signaling pathways that involve both small RNA and mRNA and affect the cell cycle, stress resistance, and developmental timing. Transposable elements, mobile genetic elements that replicate within the genome, are also thought to be stress responsive and regulated by the small RNA pathway. Therefore, we asked what the relationship was between environmental stress, diapause status, and transposable element expression in two species of agriculturally important bees, Megachile rotundata and Osmia lignaria. We characterized the TE content of the genomes of both species, then evaluated the expression of TE families during temperature stress, general environmental stress, and diapause stage. We found that the genomic TE content of the two species was very different, and M. rotundata has a larger number of annotated TEs compared to O. lignaria. We also found that both diapause stage and temperature stress had large effects on TE expression. The fold change of TE famlies tended to be larger in those expressed during diapause, however there was only a small majority that were upregulated during diapause. This suggests that stress and diapause do not break down to a simple up-regulation or down-regulation of TEs, but rather that the TE family, the genomic position of its insertions, and the exact heterochromatin formation of the organism at any given environmental state or life stage may affect overall expression of TEs.

Comparative transcriptome analysis of different developmental stage of Bactrocera minax (Diptera: Tephritidae): Implication of the molecular basis of its obligatory diapause induction

The Chinese citrus fruit fly, Bactrocera minax (Enderlein), a devastating pest in citrus, has an obligatory diapause at the pupal stage. Although the physiology of obligatory diapause has been well described, the molecular mechanisms underlying the process remain unknow. Here we investigated the molecular mechanisms of obligatory diapause induction in B. minax using high-throughput RNA-Seq data from second-instar larva (2L), third-instar larva (3L) and pupa (P) stages. A total of 116,402 unigenes were obtained, of which 54,781 unigenes were successfully annotated in public databases, and the differentially expressed genes in the 3L vs 2L, P vs 2L, and P vs 3L comparisons were identified. The cluster co-expression patterns of the differentially expressed genes revealed that significantly differentially-expressed genes in the pupal stage were predicted to be related to diapause induction. All differentially expressed genes were investigated by GO functional and KEGG pathway analysis, and the results showed that genes involved in processes such as 20-hydroxyecdysone (20E) biosynthesis, cell cycle and metabolic pathways are likely related to obligatory diapause induction in B. minax. These results provide important information on the transcriptome of the Chinese citrus fruit fly that can be used for further functional studies as well as contributing to our understanding of the molecular basis of obligatory diapause induction and suggesting potential molecular targets for the control of this pest.

Expression analysis of genes related to cold tolerance in Dendroctonus valens

Pine beetles are well known in North America for their widespread devastation of pine forests. However, Dendroctonus valens LeConte is an important invasive forest pest in China also. Adults and larvae of this bark beetle mainly winter at the trunks and roots of Pinus tabuliformis and Pinus sylvestris; larvae, in particular, result in pine weakness or even death. Since the species was introduced from the United States to Shanxi in 1998, its distribution has spread northward. In 2017, it invaded a large area at the junction of Liaoning, Inner Mongolia and Hebei provinces, showing strong cold tolerance. To identify genes relevant to cold tolerance and the process of overwintering, we sequenced the transcriptomes of wintering and non-wintering adult and larval D. valens using the Illumina HiSeq platform. Differential expression analysis methods for other non-model organisms were used to compare transcript abundances in adults and larvae at two time periods, followed by the identification of functions and metabolic pathways related to genes associated with cold tolerance. We detected 4,387 and 6,091 differentially expressed genes (DEGs) between sampling dates in larvae and adults, respectively, and 1,140 common DEGs, including genes encoding protein phosphatase, very long-chain fatty acids protein, cytochrome P450, and putative leucine-rich repeat-containing proteins. In a Gene Ontology (GO) enrichment analysis, 1,140 genes were assigned to 44 terms, with significant enrichment for cellulase activity, hydrolase activity, and carbohydrate metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) classification and enrichment analyses showed that the lysosomal and purine metabolism pathways involved the most DEGs, the highly enriched terms included autophagy-animal, pentose and glucuronate interconversions and lysosomal processes. We identified 140 candidate genes associated with cold tolerance, including genes with established roles in this trait (e.g., genes encoding trehalose transporter, fructose-1,6-bisphosphatase, and trehalase). Our comparative transcriptome analysis of adult and larval D. valens in different conditions provides basic data for the discovery of key genes and molecular mechanisms underlying cold tolerance.

Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics

BACKGROUND

The most species-rich radiation of animal life in the 66 million years following the Cretaceous extinction event is that of schizophoran flies: a third of fly diversity including Drosophila fruit fly model organisms, house flies, forensic blow flies, agricultural pest flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these flies. We use protein encoding sequence data from transcriptomes, including 3145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge.

RESULTS

Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea stat. rev. as successive sister groups to the remaining Schizophora. Ephydroidea, Drosophila's superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroborated by morphological traits, the 'Modified Oviscapt Clade' containing Tephritoidea, Nerioidea, and other families, and the 'Cleft Pedicel Clade' containing Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multispecies coalescent approaches. Rogue taxon removal was effective in increasing support values compared with strategies that maximise gene coverage or minimise missing data.

CONCLUSIONS

Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.

Steroid hormone ecdysone deficiency stimulates preparation for photoperiodic reproductive diapause

Diapause, a programmed developmental arrest primarily induced by seasonal environmental changes, is very common in the animal kingdom, and found in vertebrates and invertebrates alike. Diapause provides an adaptive advantage to animals, as it increases the odds of surviving adverse conditions. In insects, individuals perceive photoperiodic cues and modify endocrine signaling to direct reproductive diapause traits, such as ovary arrest and increased fat accumulation. However, it remains unclear as to which endocrine factors are involved in this process and how they regulate the onset of reproductive diapause. Here, we found that the long day-mediated drop in the concentration of the steroid hormone ecdysone is essential for the preparation of photoperiodic reproductive diapause in Colaphellus bowringi, an economically important cabbage beetle. The diapause-inducing long-day condition reduced the expression of ecdysone biosynthetic genes, explaining the drop in the titer of 20-hydroxyecdysone (20E, the active form of ecdysone) in female adults. Application of exogenous 20E induced vitellogenesis and ovarian development but reduced fat accumulation in the diapause-destined females. Knocking down the ecdysone receptor (EcR) in females destined for reproduction blocked reproductive development and induced diapause traits. RNA-seq and hormone measurements indicated that 20E stimulates the production of juvenile hormone (JH), a key endocrine factor in reproductive diapause. To verify this, we depleted three ecdysone biosynthetic enzymes via RNAi, which confirmed that 20E is critical for JH biosynthesis and reproductive diapause. Importantly, impairing Met function, a component of the JH intracellular receptor, partially blocked the 20E-regulated reproductive diapause preparation, indicating that 20E regulates reproductive diapause in both JH-dependent and -independent manners. Finally, we found that 20E deficiency decreased ecdysis-triggering hormone signaling and reduced JH production, thereby inducing diapause. Together, these results suggest that 20E signaling is a pivotal regulator that coordinates reproductive plasticity in response to environmental inputs.

Developmental arrest pervades organismal development and physiology where it facilitates an enormous range of adaptive responses to stressful conditions. Many animals exhibit various forms of developmental arrest that ensures survival under the most adverse environments. Reproductive diapause occurs when adults temporarily suspend reproduction in response to environmental stress and has been documented for a variety of invertebrates, particularly insects. Endocrine signals play a central role in translating environmental cues such as photoperiod into reproductive diapause-related physiology and behavior. However, it has been an unresolved issue as to which endocrine factors can respond to photoperiodic inputs and regulate diapause outputs. In this study, we found that a decrease in ecdysone levels is critical for reproductive diapause to occur. Also, ecdysone could interact with juvenile hormone to regulate the occurrence of reproductive diapause in response to photoperiodic cues. Our findings provide new insight into endocrine mechanisms of photoperiodic reproductive diapause and an example of phenotypic plasticity in animals.

Help, there are ‘omics’ in my comparative physiology!

‘Omics’ methods, such as transcriptomics, proteomics, lipidomics or metabolomics, yield simultaneous measurements of many related molecules in a sample. These approaches have opened new opportunities to generate and test hypotheses about the mechanisms underlying biochemical and physiological phenotypes. In this Commentary, we discuss general approaches and considerations for successfully integrating omics into comparative physiology. The choice of omics approach will be guided by the availability of existing resources and the time scale of the process being studied. We discuss the use of whole-organism extracts (common in omics experiments on small invertebrates) because such an approach may mask underlying physiological mechanisms, and we consider the advantages and disadvantages of pooling samples within biological replicates. These methods can bring analytical challenges, so we describe the most easily analyzed omics experimental designs. We address the propensity of omics studies to digress into ‘fishing expeditions’ and show how omics can be used within the hypothetico-deductive framework. With this Commentary, we hope to provide a roadmap that will help newcomers approach omics in comparative physiology while avoiding some of the potential pitfalls, which include ambiguous experiments, long lists of candidate molecules and vague conclusions.

Special Significance of Non-Drosophila Insects in Aging

Aging is the leading risk factor of human chronic diseases. Understanding of aging process and mechanisms facilitates drug development and the prevention of aging-related diseases. Although many aging studies focus on fruit fly as a canonical insect system, minimal attention is paid to the potentially significant roles of other insects in aging research. As the most diverse group of animals, insects provide many aging types and important complementary systems for aging studies. Insect polyphenism represents a striking example of the natural variation in longevity and aging rate. The extreme intraspecific variations in the lifespan of social insects offer an opportunity to study how aging is differentially regulated by social factors. Insect flight, as an extremely high-intensity physical activity, is suitable for the investigation of the complex relationship between metabolic rate, oxidative stress, and aging. Moreover, as a "non-aging" state, insect diapause not only slows aging process during diapause phase but also affects adult longevity during/after diapause. In the past two decades, considerable progress has been made in understanding the molecular basis of aging regulation in insects. Herein, the recent research progress in non-Drosophila insect aging was reviewed, and its potential utilization in aging in the future was discussed.

Transcriptomic changes in the pea aphid, Acyrthosiphon pisum: Effects of the seasonal timer and photoperiod

Many insect species use photoperiod as a cue for induction of seasonal responses, including seasonal polyphenism. Although most aphid species viviparously produce parthenogenetic and sexual morphs under long and short days, respectively, a seasonal timer suppresses the sexual morph production over several successive generations during a few months following hatching of a sexually produced diapause egg. To reveal the relative influences of photoperiod and the seasonal timer on the reproductive polyphenism at the gene expression level, we performed RNA sequencing-based transcriptome analyses in the pea aphid, Acyrthosiphon pisum (Hemiptera: Aphididae). Under short days, aphids with an expired seasonal timer showed a higher expression level in hundreds of genes than those with an operative seasonal timer. In contrast, aphids with an operative seasonal timer did not show upregulation in most of these genes. Functional annotations based on gene ontology showed that histone modifications and small non-coding RNA pathways were enriched in aphids with an expired seasonal timer under short-day conditions, suggesting that these epigenetic regulations on gene expression might be involved in a mechanism of maternal switching from the parthenogenetic to sexual morph production.

New Drosophila Circadian Clock Mutants Affecting Temperature Compensation Induced by Targeted Mutagenesis of Timeless

Drosophila melanogaster has served as an excellent genetic model to decipher the molecular basis of the circadian clock. Two key proteins, PERIOD (PER) and TIMELESS (TIM), are particularly well explored and a number of various arrhythmic, slow, and fast clock mutants have been identified in classical genetic screens. Interestingly, the free running period (tau, τ) is influenced by temperature in some of these mutants, whereas τ is temperature-independent in other mutant lines as in wild-type flies. This, so-called "temperature compensation" ability is compromised in the mutant timeless allele "ritsu" (tim rit ), and, as we show here, also in the tim blind allele, mapping to the same region of TIM. To test if this region of TIM is indeed important for temperature compensation, we generated a collection of new mutants and mapped functional protein domains involved in the regulation of τ and in general clock function. We developed a protocol for targeted mutagenesis of specific gene regions utilizing the CRISPR/Cas9 technology, followed by behavioral screening. In this pilot study, we identified 20 new timeless mutant alleles with various impairments of temperature compensation. Molecular characterization revealed that the mutations included short in-frame insertions, deletions, or substitutions of a few amino acids resulting from the non-homologous end joining repair process. Our protocol is a fast and cost-efficient systematic approach for functional analysis of protein-coding genes and promoter analysis in vivo. Interestingly, several mutations with a strong temperature compensation defect map to one specific region of TIM. Although the exact mechanism of how these mutations affect TIM function is as yet unknown, our in silico analysis suggests they affect a putative nuclear export signal (NES) and phosphorylation sites of TIM. Immunostaining for PER was performed on two TIM mutants that display longer τ at 25°C and complete arrhythmicity at 28°C. Consistently with the behavioral phenotype, PER immunoreactivity was reduced in circadian clock neurons of flies exposed to elevated temperatures.

Transcriptional analysis of insect extreme freeze tolerance

Few invertebrates can survive cryopreservation in liquid nitrogen, and the mechanisms by which some species do survive are underexplored, despite high application potential. Here, we turn to the drosophilid Chymomyza costata to strengthen our fundamental understanding of extreme freeze tolerance and gain insights about potential avenues for cryopreservation of biological materials. We first use RNAseq to generate transcriptomes of three C. costata larval phenotypic variants: those warm-acclimated in early or late diapause (weak capacity to survive cryopreservation), and those undergoing cold acclimation after diapause entry (extremely freeze tolerant, surviving cryopreservation). We identify mRNA transcripts representing genes and processes that accompany the physiological transition to extreme freeze tolerance and relate cryopreservation survival to the transcriptional profiles of select candidate genes using extended sampling of phenotypic variants. Enhanced capacity for protein folding, refolding and processing appears to be a central theme of extreme freeze tolerance and may allow cold-acclimated larvae to repair or eliminate proteins damaged by freezing (thus mitigating the toxicity of denatured proteins, endoplasmic reticulum stress and subsequent apoptosis). We also find a number of candidate genes (including both known and potentially novel, unannotated sequences) whose expression profiles tightly mirror the change in extreme freeze tolerance status among phenotypic variants.

Noncoding RNA Regulation of Dormant States in Evolutionarily Diverse Animals

Dormancy is evolutionarily widespread and can take many forms, including diapause, dauer formation, estivation, and hibernation. Each type of dormancy is characterized by distinct features; but accumulating evidence suggests that each is regulated by some common processes, often referred to as a common "toolkit" of regulatory mechanisms, that likely include noncoding RNAs that regulate gene expression. Noncoding RNAs, especially microRNAs, are well-known regulators of biological processes associated with numerous dormancy-related processes, including cell cycle progression, cell growth and proliferation, developmental timing, metabolism, and environmental stress tolerance. This review provides a summary of our current understanding of noncoding RNAs and their involvement in regulating dormancy.

Diapause-associated changes in the lipid and metabolite profiles of the Asian tiger mosquito, Aedes albopictus

Diapause is an alternative life-history strategy that allows organisms to enter developmental arrest in anticipation of unfavorable conditions. Diapause is widespread among insects and plays a key role in enhancing overwinter survival as well as defining the seasonal and geographic distributions of populations. Next-generation sequencing has greatly advanced our understanding of the transcriptional basis for this crucial adaptation but less is known about the regulation of embryonic diapause physiology at the metabolite level. Here, we characterized the lipid and metabolite profiles of embryonic diapause in the Asian tiger mosquito, Aedes albopictus We used an untargeted approach to capture the relative abundance of 250 lipids and 241 metabolites. We observed adjustments associated with increased energy storage, including an accumulation of lipids, the formation of larger lipid droplets and increased lipogenesis, as well as metabolite shifts suggesting reduced energy utilization. We also found changes in neuroregulatory- and insulin-associated metabolites with potential roles in diapause regulation. Finally, we detected a group of unidentified, diapause-specific metabolites which have physical properties similar to those of steroids/steroid derivatives and may be associated with the ecdysteroidal regulation of embryonic diapause in A.albopictus Together, these results deepen our understanding of the metabolic regulation of embryonic diapause and identify key targets for future investigations.

Transcriptome Analysis Reveals Candidate Genes for Cold Tolerance in Drosophila ananassae

Coping with daily and seasonal temperature fluctuations is a key adaptive process for species to colonize temperate regions all over the globe. Over the past 18,000 years, the tropical species Drosophila ananassae expanded its home range from tropical regions in Southeast Asia to more temperate regions. Phenotypic assays of chill coma recovery time (CCRT) together with previously published population genetic data suggest that only a small number of genes underlie improved cold hardiness in the cold-adapted populations. We used high-throughput RNA sequencing to analyze differential gene expression before and after exposure to a cold shock in cold-tolerant lines (those with fast chill coma recovery, CCR) and cold-sensitive lines (slow CCR) from a population originating from Bangkok, Thailand (the ancestral species range). We identified two candidate genes with a significant interaction between cold tolerance and cold shock treatment: GF14647 and GF15058. Further, our data suggest that selection for increased cold tolerance did not operate through the increased activity of heat shock proteins, but more likely through the stabilization of the actin cytoskeleton and a delayed onset of apoptosis.

Cell cycle regulator, small silencing RNA, and segmentation patterning gene expression in relation to embryonic diapause in the band-legged ground cricket

Insects enter diapause to synchronize their life cycle with biotic and abiotic conditions favorable for their development, reproduction, and survival. Adult females of the band-legged ground cricket Dianemobius nigrofasciatus (Orthoptera, Glyllidae) respond to environmental factors in autumn and lay diapause-destined eggs. The eggs arrest their development and enter diapause at a very early embryonic stage, specifically the cellular blastoderm. To elucidate the physiological mechanisms underlying this very early stage programmed developmental arrest, we investigated the cell division cycle as well as the expression of cell cycle regulators, small silencing RNAs, and segment patterning genes. The diapause embryo arrests its cell cycle predominantly at the G₀/G₁ phase. The proportion of cells in the S phase of the cell cycle abruptly decreased at the time of developmental arrest, but further changes of the G₀/G₁ and G₂/M were later observed. Thus, cell cycle arrest in the diapause embryo is not an immediate event, but it takes longer to reach the steady state. We further elucidated molecular events possibly involved in diapause preparation and entry. Downregulation of Proliferating cellular antigen (PCNA; a cell cycle regulator), caudal and pumilio (cad and pum; early segmentation genes) as well as P-element induced wimpy testis (piwi) (a small silencing RNA) prior to the onset of developmental arrest was notable. The downregulation of PCNA, cad and pum continued even after entry into developmental arrest. In contrast to upregulation in non-diapause eggs, Cyclin D (another cell cycle regulator) and hunchback, Krüppel, and runt (gap and pair-rule genes) were downregulated in diapause eggs. These molecular events may contribute to embryonic diapause of D. nigrofasciatus.

Expression profiles of 14 small heat shock protein (sHSP) transcripts during larval diapause and under thermal stress in the spruce budworm, Choristoneura fumiferana (L.)

Diapause is an important strategy for certain insect species to survive unfavorable environmental conditions, including low temperatures experienced when they overwinter in cold climate. Many studies have indicated that the increased expression of heat shock proteins during diapause improves the thermal tolerance of insects. However, the relationship between small heat shock proteins (sHSPs) and diapause is not clear or well-researched. In this study, we investigated the transcript levels of 14 sHSP genes in the spruce budworm, Choristoneura fumiferana, a major pest of spruce and fir in Canada, during pre-diapause, diapause, and post-diapause under normal rearing conditions and in response to a heat shock treatment. We found that sHSP expression profiles could be classified into five patterns under normal laboratory conditions: pattern I was upregulated only during pre-diapause, pattern II was upregulated only during diapause, pattern III was constantly expressed throughout diapause, pattern IV was upregulated in both pre-diapause and diapause, and pattern V was upregulated only during post-diapause. After heat shock, five different expression patterns were observed: pattern I responded weakly or not at all throughout diapause, pattern II responded weakly during the diapause stage but strongly at the onset of diapause and in the post-diapause period, pattern III was upregulated only during post-diapause, pattern IV was strongest during diapause, and pattern V was strongest only in early diapause. These complex expression profiles lead us to suggest that most of the sHSP genes are involved in the diapause process and that they may have multiple and important roles in different phases of this process.

How crickets become freeze tolerant: The transcriptomic underpinnings of acclimation in Gryllus veletis

Some ectotherms can survive internal ice formation. In temperate regions, freeze tolerance is often induced by decreasing temperature and/or photoperiod during autumn. However, we have limited understanding of how seasonal changes in physiology contribute to freeze tolerance, and how these changes are regulated. During a six week autumn-like acclimation, late-instar juveniles of the spring field cricket Gryllus veletis (Orthoptera: Gryllidae) become freeze tolerant, which is correlated with accumulation of low molecular weight cryoprotectants, elevation of the temperature at which freezing begins, and metabolic rate suppression. We used RNA-Seq to assemble a de novo transcriptome of this emerging laboratory model for freeze tolerance research. We then focused on gene expression during acclimation in fat body tissue due to its role in cryoprotectant production and regulation of energetics. Acclimated G. veletis differentially expressed >3000 transcripts in fat body. This differential expression may contribute to metabolic suppression in acclimated G. veletis, but we did not detect changes in expression that would support cryoprotectant accumulation or enhanced control of ice formation, suggesting that these latter processes are regulated post-transcriptionally. Acclimated G. veletis differentially regulated transcripts that likely coordinate additional freeze tolerance mechanisms, including upregulation of enzymes that may promote membrane and cytoskeletal remodelling, cryoprotectant transporters, cytoprotective proteins, and antioxidants. Thus, while accumulation of cryoprotectants and controlling ice formation are commonly associated with insect freeze tolerance, our results support the hypothesis that many other systems contribute to surviving internal ice formation. Together, this information suggests new avenues for understanding the mechanisms underlying insect freeze tolerance.

Divergence in larval diapause induction between the rice and water-oat populations of the striped stem borer, Chilo suppressalis (Walker) (Lepidoptera: Crambidae)

Differences in diapause traits can result in the seasonal reproductive isolation of host plant-associated insect populations and thereby facilitate the population divergence. The striped stem borer, Chilo suppressalis, has two host plant-associated populations: rice population and water-oat population. Several studies have found evidence that seasonal reproductive isolation between these populations is at least partially due to interpopulation differences in diapause. However, there still lack unambiguous evidence comparing characteristics of diapause induction for both populations. We compared the photoperiodic response and the age of peak photoperiod sensitivity of these populations and used RNA-Seq to compare the molecular response of diapause induction between populations. The photoperiodic response of the two populations differed at 25 °C; the critical night length of larvae from the rice population was 11 h and 20 min, whereas no obvious critical night length was in those from the water-oat population. In rice population, larvae were most sensitive to photoperiod at 9-12 days of age, whereas in water-oat population, larvae were the most sensitive to photoperiod at 9-10 days of age. The RNA-Seq results indicated that there were several differences in the molecular response of diapause induction and small overlap in differentially expressed genes (DEGs) between populations. Furthermore, GO analysis indicated that both rice and water-oat population's DEGs were significantly enriched in heme and iron binding. Besides, water-oat population's DEGs were significantly enriched in metabolizing nutrients but rice population's DEGs do not. Thus, our results described differences in diapause induction between rice and water-oat populations of C. suppressalis which could affect the timing of diapause and thereby contribute to the seasonal reproductive isolation of these host plant-associated populations. In conclusion, this work suggests that difference in diapause induction could promote the population divergence in insects associated with different host plants.

Requirement of Leptinotarsa decemlineata gene within the 74EF puff for larval-pupal metamorphosis and appendage growth

Two Drosophila melanogaster E-twenty-six domain transcription factor isoforms (E74A and E74B) act differentially at the start of the 20-hydroxyecdysone (20E) signalling cascade to regulate larval-pupal metamorphosis. In the present paper, we identified the two isoforms (LdE74A and LdE74B) in Leptinotarsa decemlineata. During the larval development stage, the mRNA transcript levels of the two LdE74 isoforms were correlated with circulating 20E titres. In vitro midgut culture and in vivo dietary supplementation with 20E revealed that the presence of 20E induced expression peaks of both LdE74A and LdE74B, with similar patterns observed for the two isoforms. Moreover, the mRNA transcript levels of both LdE74A and LdE74B isoforms were significantly downregulated in the L. decemlineata ecdysone receptor RNA interference (RNAi) specimens, but not in the LdE75 RNAi beetles. Ingestion of 20E reduced the larval fresh weights and shortened the larval development period, irrespective of knockdown of LdE74 or not. RNAi of LdE74 did not affect 20E-induced expression of the Ecdysone induced protein 75-hormone receptor 3-fushi tarazu factor 1 (E75-HR3-FTZ-F1) transcriptional cascade. Thus, it seems that LdE74 mediates 20E signalling independent of the E75-HR3-FTZ-F1 transcriptional cascade. Furthermore, silencing of both LdE74 isoforms caused failure of ecdysis. Most of the LdE74 RNAi beetles remained as prepupae. The LdE74 RNAi prepupae exhibited adult character-like forms underneath after removal of the apolysed larval cuticle. Their appendages such as antennae, legs and wings were shorter than those of control larvae. Only a few LdE74 RNAi larvae finally became deformed pupae, with shortened antennae and legs. Therefore, LdE74 is required for larval-pupal metamorphosis and appendage growth in L. decemlineata.

Diapause in a tropical oil-collecting bee: molecular basis unveiled by RNA-Seq

BACKGROUND

Diapause is a natural phenomenon characterized by an arrest in development that ensures the survival of organisms under extreme environmental conditions. The process has been well documented in arthropods. However, its molecular basis has been mainly studied in species from temperate zones, leaving a knowledge gap of this phenomenon in tropical species. In the present study, the Neotropical and solitary bee Tetrapedia diversipes was employed as a model for investigating diapause in species from tropical zones. Being a bivoltine insect, Tetrapedia diversipes produce two generations of offspring per year. The first generation, normally born during the wet season, develops faster than individuals from the second generation, born after the dry season. Furthermore, it has been shown that the development of the progeny, of the second generation, is halted at the 5th larval instar, and remains in larval diapause during the dry season. Towards the goal of gaining a better understanding of the diapause phenomenon we compared the global gene expression pattern, in larvae, from both reproductive generations and during diapause. The results demonstrate that there are similarities in the observed gene expression patterns to those already described for temperate climate models, and also identify diapause-related genes that have not been previously reported in the literature.

RESULTS

The RNA-Seq analysis identified 2275 differentially expressed transcripts, of which 1167 were annotated. Of these genes, during diapause, 352 were upregulated and 815 were downregulated. According to their biological functions, these genes were categorized into the following groups: cellular detoxification, cytoskeleton, cuticle, sterol and lipid metabolism, cell cycle, heat shock proteins, immune response, circadian clock, and epigenetic control.

CONCLUSION

Many of the identified genes have already been described as being related to diapause; however, new genes were discovered, for the first time, in this study. Among those, we highlight: Niemann-Pick type C1, NPC2 and Acyl-CoA binding protein homolog (all involved in ecdysteroid synthesis); RhoBTB2 and SASH1 (associated with cell cycle regulation) and Histone acetyltransferase KAT7 (related to epigenetic transcriptional regulation). The results presented here add important findings to the understanding of diapause in tropical species, thus increasing the comprehension of diapause-related molecular mechanisms.

Cell cycle arrest in the jewel wasp Nasonia vitripennis in larval diapause

Insects enter diapause to synchronise their life cycle with biotic and abiotic environmental conditions favourable for their development, reproduction, and survival. One of the most noticeable characteristics of diapause is the blockage of ontogeny. Although this blockage should occur with the cessation of cellular proliferation, i.e. cell cycle arrest, it was confirmed only in a few insect species and information on the molecular pathways involved in cell cycle arrest is limited. In the present study, we investigated developmental and cell cycle arrest in diapause larvae of the jewel wasp Nasonia vitripennis. Developmental and cell cycle arrest occur in the early fourth instar larval stage of N. vitripennis under short days. By entering diapause, the S fraction of the cell cycle disappears and approximately 80% and 20% of cells arrest their cell cycle in the G0/G1 and G2 phases, respectively. We further investigated expression of cell cycle regulatory genes and some housekeeping genes to dissect molecular mechanisms underlying the cell cycle arrest.

Recovery from supercooling, freezing, and cryopreservation stress in larvae of the drosophilid fly, Chymomyza costata

Physiological adjustments accompanying insect cold acclimation prior to cold stress have been relatively well explored. In contrast, recovery from cold stress received much less attention. Here we report on recovery of drosophilid fly larvae (Chymomyza costata) from three different levels of cold stress: supercooling to −10 °C, freezing at −30 °C, and cryopreservation at −196 °C. Analysis of larval CO₂ production suggested that recovery from all three cold stresses requires access to additional energy reserves to support cold-injury repair processes. Metabolomic profiling (targeting 41 metabolites using mass spectrometry) and custom microarray analysis (targeting 1,124 candidate mRNA sequences) indicated that additional energy was needed to: clear by-products of anaerobic metabolism, deal with oxidative stress, re-fold partially denatured proteins, and remove damaged proteins, complexes and/or organelles. Metabolomic and transcriptomic recovery profiles were closely similar in supercooled and frozen larvae, most of which successfully repaired the cold injury and metamorphosed into adults. In contrast, the majority of cryopreseved larvae failed to proceed in ontogenesis, showed specific metabolic perturbations suggesting impaired mitochondrial function, and failed to up-regulate a set of 116 specific genes potentially linked to repair of cold injury.

Global Transcriptome Sequencing Reveals Molecular Profiles of Summer Diapause Induction Stage of Onion Maggot, Delia antiqua (Diptera: Anthomyiidae)

The onion maggot, Delia antiqua, is a worldwide subterranean pest and can enter diapause during the summer and winter seasons. The molecular regulation of the ontogenesis transition remains largely unknown. Here we used high-throughput RNA sequencing to identify candidate genes and processes linked to summer diapause (SD) induction by comparing the transcriptome differences between the most sensitive larval developmental stage of SD and nondiapause (ND). Nine pairwise comparisons were performed, and significantly differentially regulated transcripts were identified. Several functional terms related to lipid, carbohydrate, and energy metabolism, environmental adaption, immune response, and aging were enriched during the most sensitive SD induction period. A subset of genes, including circadian clock genes, were expressed differentially under diapause induction conditions, and there was much more variation in the most sensitive period of ND- than SD-destined larvae. These expression variations probably resulted in a deep restructuring of metabolic pathways. Potential regulatory elements of SD induction including genes related to lipid, carbohydrate, energy metabolism, and environmental adaption. Collectively, our results suggest the circadian clock is one of the key drivers for integrating environmental signals into the SD induction. Our transcriptome analysis provides insight into the fundamental role of the circadian clock in SD induction in this important model insect species, and contributes to the in-depth elucidation of the molecular regulation mechanism of insect diapause induction.

MicroRNAs are differentially abundant during Aedes albopictus diapause maintenance but not diapause induction

Diapause is a programmed dormancy that allows organisms to tolerate predictable periods of unfavourable conditions by temporarily halting development and reducing metabolism. Diapause is widespread amongst insects and is crucial for allowing organisms to coordinate their growth and reproduction with favourable environmental conditions. Although the adaptive significance of diapause is well understood, the molecular mechanisms underpinning diapause remain unresolved. We performed high-throughput sequencing to investigate the role of microRNAs (miRNAs) in the diapause of the Asian tiger mosquito, Aedes albopictus. We first investigated miRNAs in diapause induction by characterizing maternally provisioned miRNAs in mature oocytes of Ae. albopictus under diapause-inducing and diapause-averting conditions. Second, we investigated miRNAs in diapause maintenance by characterizing miRNAs in diapause and nondiapause pharate larvae. We identified 162 miRNAs, 152 previously known and 10 putatively novel. We identified no differentially abundant miRNAs in mature oocytes and seven differentially abundant miRNAs in pharate larvae. The predicted targets of differentially abundant miRNAs include genes affecting several processes related to diapause maintenance including ecdysone regulation, immune response, lipid metabolism and regulation of development. Our results suggest that Ae. albopictus does not maternally provision a unique set of miRNAs during diapause induction but miRNAs are a component of diapause maintenance in this species.

Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate

Numerous aquatic invertebrates remain dormant for decades in a hydrated state as encysted embryos. In search for functional pathways associated with this form of dormancy, we used label-free quantitative proteomics to compare the proteomes of hydrated encysted dormant embryos (resting eggs; RE) with nondormant embryos (amictic eggs; AM) of the rotifer Brachionus plicatilisA total of 2631 proteins were identified in rotifer eggs. About 62% proteins showed higher abundance in AM relative to RE (Fold Change>3; p = 0.05). Proteins belonging to numerous putative functional pathways showed dramatic changes during dormancy. Most striking were changes in the mitochondria indicating an impeded metabolism. A comparison between the abundance of proteins and their corresponding transcript levels, revealed higher concordance for RE than for AM. Surprisingly, numerous highly abundant dormancy related proteins show corresponding high mRNA levels in metabolically inactive RE. As these mRNAs and proteins degrade at the time of exit from dormancy they may serve as a source of nucleotides and amino acids during the exit from dormancy. Because proteome analyses point to a similarity in functional pathways of hydrated RE and desiccated life forms, REs were dried. Similar hatching and reproductive rates were found for wet and dried REs, suggesting analogous pathways for long-term survival in wet or dry forms. Analysis by KEGG pathways revealed a few general strategies for dormancy, proposing an explanation for the low transcriptional similarity among dormancies across species, despite the resemblance in physiological phenotypes.

Conceptual framework of the eco-physiological phases of insect diapause development justified by transcriptomic profiling

Insects often overcome unfavorable seasons in a hormonally regulated state of diapause during which their activity ceases, development is arrested, metabolic rate is suppressed, and tolerance of environmental stress is bolstered. Diapausing insects pass through a stereotypic succession of eco-physiological phases termed "diapause development." The phasing is varied in the literature, and the whole concept is sometimes criticized as being too artificial. Here we present the results of transcriptional profiling using custom microarrays representing 1,042 genes in the drosophilid fly, Chymomyza costata Fully grown, third-instar larvae programmed for diapause by a photoperiodic (short-day) signal were assayed as they traversed the diapause developmental program. When analyzing the gradual dynamics in the transcriptomic profile, we could readily distinguish distinct diapause developmental phases associated with induction/initiation, maintenance, cold acclimation, and termination by cold or by photoperiodic signal. Accordingly, each phase is characterized by a specific pattern of gene expression, supporting the physiological relevance of the concept of diapause phasing. Further, we have dissected in greater detail the changes in transcript levels of elements of several signaling pathways considered critical for diapause regulation. The phase of diapause termination is associated with enhanced transcript levels in several positive elements stimulating direct development (the 20-hydroxyecdysone pathway: Ecr, Shd, Broad; the Wnt pathway: basket, c-jun) that are countered by up-regulation in some negative elements (the insulin-signaling pathway: Ilp8, PI3k, Akt; the target of rapamycin pathway: Tsc2 and 4EBP; the Wnt pathway: shaggy). We speculate such up-regulations may represent the early steps linked to termination of diapause programming.

Identification of ecdysteroidogenic enzyme genes and their expression during pupal diapause in the cabbage armyworm, Mamestra brassicae

In this study, we identified ecdysteroidogenic enzymes in the cabbage armyworm, Mamestra brassicae, and demonstrated reduced expression of these genes during diapause. Some insects employ a temporary developmental arrest, diapause, to survive in severe environments. The titres of the moulting hormone ecdysteroid were reduced in diapause pupae of M. brassicae; therefore, ecdysteroidogenesis might be suppressed by a diapause-specific mechanism. To clarify expression changes of ecdysteroidogenic enzyme genes during diapause in M. brassicae, we first identified the genes for seven ecdysteroidogenic enzymes: Neverland, Non-molting glossy (Nm-g), CYP307A1 (Spook), CYP306A1 (Phantom), CYP302A1 (Disembodied), CYP315A1 (Shadow) and CYP314A1 (Shade). Enzymatic assays using heterologous expression in Drosophila Schneider 2 (S2) cells and analysis of mRNA distribution indicated that the identified genes were ecdysteroidogenic enzymes of M. brassicae. Expression levels of these ecdysteroidogenic enzyme genes were compared between prothoracic glands in different pupal stages throughout diapause. Immediately after pupation, diapause-destined pupae showed similar expression levels of ecdysteroidogenic enzyme genes to those of nondiapause pupae. All of these genes showed reduced gene expression after diapause initiation. Expression was immediately increased in diapause-destined pupae at the postdiapause quiescence phase. These results indicate that reduced expression of ecdysteroidogenic enzyme genes suppresses ecdysteroidogenesis and maintains developmental arrest during diapause.

Cold tolerance of the Asian tiger mosquito Aedes albopictus and its response to epigenetic alterations

Phenotypic plasticity is considered as one of the key traits responsible for the establishment of populations of the invasive mosquito Aedes albopictus, an important vector of viral and parasitic pathogens. The successful spread of this species to higher altitudes and latitudes may be explained by its ability to rapidly induce a heritable low-temperature phenotype (cold hardiness in eggs). As a result of the low genetic diversity of founder populations, an epigenetic short-term mechanism has been suggested as the driver of this diversification. We investigated if random epigenetic alterations promoted the cold hardiness of Ae. albopictus eggs from a transgenerational study of two epigenetic agents (genistein and vinclozolin). To this end, we evaluated changes in lethal time for 50% of pharate larvae (Lt₅₀) from eggs exposed to -2°C in two subsequent generations that used a new dose-response test design. We detected a significant diversification of the cold hardiness of eggs (up to 64.5%) that was associated with the epigenetic change in the two subsequent offspring generations. An effect size of epigenetically modulated cold hardiness of this magnitude is likely to have an impact on the spatial distribution of this species. Our results provide a framework for further research on epigenetic temperature adaptation of invasive species to better explain and predict their rapid range expansions.

Describing the Diapause-Preparatory Proteome of the Beetle Colaphellus bowringi and Identifying Candidates Affecting Lipid Accumulation Using Isobaric Tags for Mass Spectrometry-Based Proteome Quantification (iTRAQ)

Prior to entering diapause, insects must prepare themselves physiologically to withstand the stresses of arresting their development for a lengthy period. While studies describing the biochemical and cellular milieu of the maintenance phase of diapause are accumulating, few studies have taken an “omics” approach to describing molecular events during the diapause preparatory phase. We used isobaric tags and mass spectrometry (iTRAQ) to quantitatively compare the expression profiles of proteins identified during the onset of diapause preparation phase in the heads of adult female cabbage beetles, Colaphellus bowringi. A total of 3,175 proteins were identified, 297 of which were differentially expressed between diapause-destined and non-diapause-destined female adults and could therefore be involved in diapause preparation in this species. Comparison of identified proteins with protein function databases shows that many of these differentially expressed proteins enhanced in diapause destined beetles are involved in energy production and conversion, carbohydrate metabolism and transport, and lipid metabolism. Further hand annotation of differentially abundant peptides nominates several associated with stress hardiness, including HSPs and antioxidants, as well as neural development. In contrast, non-diapause destined beetles show substantial increases in cuticle proteins, suggesting additional post-emergence growth. Using RNA interference to silence a fatty acid-binding protein (FABP) that was highly abundant in the head of diapause-destined females prevented the accumulation of lipids in the fat body, a common product of diapause preparation in this species and others. Surprisingly, RNAi against the FABP also affected the transcript abundance of several heat shock proteins. These results suggest that the identified differentially expressed proteins that play vital roles in lipid metabolism may also contribute somehow to enhanced hardiness to environmental stress that is characteristic of diapause.

Physiological and molecular mechanisms underlying photoperiodism in the spider mite: comparisons with insects

Photoperiodism is an adaptive, seasonal timing system that enables organisms to coordinate their development and physiology to annual changes in the environment using day length (photoperiod) as a cue. This review summarizes our knowledge of the physiological mechanisms underlying photoperiodism in spider mites. In particular, the two-spotted spider mite Tetranychus urticae is focussed, which has long been used as a model species for studying photoperiodism. Photoperiodism is established by several physiological modules, such as the photoreceptor, photoperiodic time measurement system, counter system, and endocrine effector. It is now clear that retinal photoreception through the ocelli is indispensable for the function of photoperiodism, at least in T. urticae. Visual pigment, which comprised opsin protein and a vitamin A-based pigment, is involved in photoreception. The physiological basis of the photoperiodic time measurement system is still under debate, and we have controversial evidence for the hourglass-based time measurement and the oscillator-based time measurement. Less attention has been centred on the counter system in insects and mites. Mite reproduction is possibly regulated by the ecdysteroid, ponasterone A. Prior physiological knowledge has laid the foundation for the next steps essential for the elucidation of the molecular mechanisms driving photoperiodism.

Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome

Cold tolerance is a key determinant of insect distribution and abundance, and thermal acclimation can strongly influence organismal stress tolerance phenotypes, particularly in small ectotherms like Drosophila. However, there is limited understanding of the molecular and biochemical mechanisms that confer such impressive plasticity. Here, we use high-throughput mRNA sequencing (RNA-seq) and liquid chromatography – mass spectrometry (LC-MS) to compare the transcriptomes and metabolomes of D. melanogaster acclimated as adults to warm (rearing) (21.5 °C) or cold conditions (6 °C). Cold acclimation improved cold tolerance and led to extensive biological reorganization: almost one third of the transcriptome and nearly half of the metabolome were differentially regulated. There was overlap in the metabolic pathways identified via transcriptomics and metabolomics, with proline and glutathione metabolism being the most strongly-supported metabolic pathways associated with increased cold tolerance. We discuss several new targets in the study of insect cold tolerance (e.g. dopamine signaling and Na⁺-driven transport), but many previously identified candidate genes and pathways (e.g. heat shock proteins, Ca²⁺ signaling, and ROS detoxification) were also identified in the present study, and our results are thus consistent with and extend the current understanding of the mechanisms of insect chilling tolerance.

Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

Duration of dormancy regulates seasonal timing in many organisms and may be modulated by day length and temperature. Though photoperiodic modulation has been well studied, temperature modulation of dormancy has received less attention. Here, we leverage genetic variation in diapause in the apple maggot fly, Rhagoletis pomonella, to test whether gene expression during winter or following spring warming regulates diapause duration. We used RNAseq to compare transcript abundance during and after simulated winter between an apple-infesting population and a hawthorn-infesting population where the apple population ends pupal diapause earlier than the hawthorn-infesting population. Marked differences in transcription between the two populations during winter suggests that the ‘early’ apple population is developmentally advanced compared to the ‘late’ hawthorn population prior to spring warming, with transcripts participating in growth and developmental processes relatively up-regulated in apple pupae during the winter cold period. Thus, regulatory differences during winter ultimately drive phenological differences that manifest themselves in the following summer. Expression and polymorphism analysis identify candidate genes in the Wnt and insulin signaling pathways that contribute to population differences in seasonality. Both populations remained in diapause and displayed a pattern of up- and then down-regulation (or vice versa) of growth-related transcripts following warming, consistent with transcriptional repression. The ability to repress growth stimulated by permissive temperatures is likely critical to avoid mismatched phenology and excessive metabolic demand. Compared to diapause studies in other insects, our results suggest some overlap in candidate genes/pathways, though the timing and direction of changes in transcription are likely species-specific.