Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects

Novel observations of "freeze resistance" and dynamic blue and green dorsal coloration in frozen and thawing Dryophytes chrysoscelis

Freeze tolerant animals survive the winter by tolerating the freezing and thawing of up to 70% of body water and the respective cessation and resumption of essential functions including circulation and respiration during each freeze-thaw cycle. Cope's gray treefrog Dryophytes chrysoscelis is a freeze tolerant anuran that uses a system of cryoprotectants to prevent intracellular freezing and mitigate osmotic stress during freezing and thawing episodes. Morphological features were documented in D. chrysoscelis using a repeated freeze-thaw protocol. Dorsal skin in frozen frogs was distinctly blue and green before reverting to brown during thawing. The dorsal color change in frozen frogs does not function similarly to other known color change events in amphibians. The return to brown skin color in thawing animals coincides with recovery of vital functions in freeze tolerant frogs, suggesting that dorsal color change is an indicator of postfreeze recovery in D. chrysoscelis. We also provide evidence of "freeze resistance" in D. chrysoscelis. Two individuals did not freeze following three successive bouts of ice inoculation at -2.5°C and maintained brown dorsal color despite ice crystallization on the dorsum and contact with frozen substrate. Both frogs had similar plasma osmolality, circulating cryoprotectants, and incidence of cryoinjury compared to frogs that were frozen and thawed once or three times. Freeze resistance may be explained by physical changes in the skin including lipid accumulation and dehydration. This integrative study presents novel attributes of organismal freeze tolerance in D. chrysoscelis.

Genomic adaptive potential to cold environments in the invasive red swamp crayfish

Biological invasion refers to the introduction, spread, and establishment of non-native species in a novel habitat. The ways in which invasive species successfully colonize new and different environments remain a fundamental topic of research in ecology and evolutionary biology. Here, we investigated the genomic and transcriptomic characteristics of the red swamp crayfish (Procambarus clarkii), a widespread invader in freshwater environments. Targeting a recently colonized population in Sapporo, Japan that appears to have acquired a high degree of cold tolerance, RNA-seq analysis revealed differentially expressed genes in response to cold exposure, and those involved in protease inhibitors and cuticle development were considered top candidates. We also found remarkable duplications for these gene families during evolution and their concerted expression patterns, suggesting functional amplification against low temperatures. Our study thus provides clues to the unique genetic characteristics of P. clarkii, possibly related to cold adaptation.

Comparative transcriptome analysis of Callosobruchus chinensis (L.) (Coleoptera: Chrysomelidae-Bruchinae) after heat and cold stress exposure

Callosobruchus chinensis is regarded as one of the cosmopolitan pests of legume crops and can cause tremendous losses to a variety of beans. This study focused on comparative transcriptome analyses of C. chinensis exposed to 45 °C (heat stress), 27 °C (ambient temperature) and -3 °C (cold stress) for 3 h to investigate the gene differences and underlying molecular mechanisms. There were 402 and 111 differentially expressed genes (DEGs) identified in the heat and cold stress treatments, respectively. "cell process", "cell" and "binding" were the main enriched functions and biological processes revealed by gene ontology (GO) analysis. The clusters of orthologous genes (COG) showed that DEGs were assigned to the categories: "posttranslational modification, protein turnover, chaperones", "lipid transport and metabolism", and "general function prediction only". With respect to the Kyoto Encyclopedia of Genes and Genomes (KEGG), the "longevity regulating pathway-multiple species", "carbon metabolism", "peroxisome", "protein processing in endoplasmic", "glyoxylate and dicarboxylate metabolism" pathways were significantly enriched. The annotation and enrichment analysis revealed that genes encoding heat shock proteins (Hsps) and cuticular proteins were significantly upregulated under high and low-temperature stresses, respectively. In addition, some DEGs encoding "Protein lethal essential for life", "Reverse transcriptase", "DnaJ domain", "Cytochrome" and "Zinc finger protein" were also upregulated to varying degrees. Transcriptomic data were validated using qRT‒PCR, which confirmed that they were consistent. In this paper, the temperature tolerance of C. chinensis adults was evaluated and the results showed that female adults were more sensitive to heat and cold stress than males, and the upregulation of heat shock protein and epidermal protein was the largest in DEGs after heat and cold stress, respectively. These findings provide a reference for further understanding the biological characteristics of C. chinensis adults and the molecular mechanisms underlying the response to low and high temperatures.

Insect Freeze-Tolerance Downunder: The Microbial Connection

Insects that are freeze-tolerant start freezing at high sub-zero temperatures and produce small ice crystals. They do this using ice-nucleating agents that facilitate intercellular ice growth and prevent formation of large crystals where they can damage tissues. In Aotearoa/New Zealand the majority of cold adapted invertebrates studied survive freezing at any time of year, with ice formation beginning in the rich microbiome of the gut. Some freeze-tolerant insects are known to host symbiotic bacteria and/or fungi that produce ice-nucleating agents and we speculate that gut microbes of many New Zealand insects may provide ice-nucleating active compounds that moderate freezing. We consider too the possibility that evolutionary disparate freeze-tolerant insect species share gut microbes that are a source of ice-nucleating agents and so we describe potential transmission pathways of shared gut fauna. Despite more than 30 years of research into the freeze-tolerant mechanisms of Southern Hemisphere insects, the role of exogenous ice-nucleating agents has been neglected. Key traits of three New Zealand freeze-tolerant lineages are considered in light of the supercooling point (temperature of ice crystal formation) of microbial ice-nucleating particles, the initiation site of freezing, and the implications for invertebrate parasites. We outline approaches that could be used to investigate potential sources of ice-nucleating agents in freeze-tolerant insects and the tools employed to study insect microbiomes.

Key questions on the evolution and biogeography of New Zealand alpine insects

New Zealand alpine environments host a diverse assemblage of insect lineages, with virtually every major insect group represented. The modern mountain ranges of New Zealand are relatively young and large areas of habitat above the tree line have only been in continual existence for the past one million years. We discuss the geological history and physical characteristics of New Zealand alpine environments and the resulting selective pressures placed on insect species. Some notable alpine taxa and previous faunistic research is highlighted. We discuss examples where single lineages have colonised the alpine zone and contrast these with larger radiations of alpine species which in some cases are the result of multiple colonisation events. The age of most alpine lineages is consistent with the young geological age of the mountains, nevertheless there are some much older alpine lineages of uncertain evolutionary history. We show that alpine species have employed a very broad range of morphological, physiological, and behavioural adaptations to survive in the alpine zone, and new studies are starting to unpick their genomic basis. Finally, we look to the future and assess threats to the unique New Zealand alpine insect fauna.

Exploring Cold Hardiness within a Butterfly Clade: Supercooling Ability and Polyol Profiles in European Satyrinae

The cold hardiness of overwintering stages affects the distribution of temperate and cold-zone insects. Studies on Erebia, a species-rich cold-zone butterfly genus, detected unexpected diversity of cold hardiness traits. We expanded our investigation to eight Satyrinae species of seven genera. We assessed Autumn and Winter supercooling points (SCPs) and concentrations of putatively cryoprotective sugars and polyols via gas chromatography–mass spectrometry. Aphantopus hyperantus and Hipparchia semele survived freezing of body fluids; Coenonympha arcania, C. gardetta, and Melanargia galathea died prior to freezing; Maniola jurtina, Chazara briseis, and Minois dryas displayed a mixed response. SCP varied from −22 to −9 °C among species. Total sugar and polyol concentrations (TSPC) varied sixfold (2 to 12 μg × mg−1) and eightfold including the Erebia spp. results. SCP and TSPC did not correlate. Alpine Erebia spp. contained high trehalose, threitol, and erythritol; C. briseis and C. gardetta contained high ribitol and trehalose; lowland species contained high saccharose, maltose, fructose, and sorbitol. SCP, TSPC, and glycerol concentrations were affected by phylogeny. Species of mountains or steppes tend to be freeze-avoidant, overwinter as young larvae, and contain high concentrations of trehalose, while those of mesic environments tend to be freeze-tolerant, overwinter as later instars, and rely on compounds such as maltose, saccharose, and fructose.

A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation

The hyperdiverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome evolution of beetles, as well as genetic changes associated with specialization to high-elevation alpine habitats. In particular, this genome resource provides a foundation for expanding comparative molecular research into mechanisms of insect cold adaptation. Comparison to other beetles shows a strong signature of genome compaction, with N. riversi possessing a relatively small genome (~147 Mb) compared to other beetles, with associated reductions in repeat element content and intron length. Small genome size is not, however, associated with fewer protein-coding genes, and an analysis of gene family diversity shows significant expansions of genes associated with cellular membranes and membrane transport, as well as protein phosphorylation and muscle filament structure. Finally, our genomic analyses show that these high-elevation beetles have endosymbiotic Spiroplasma, with several metabolic pathways (e.g., propanoate biosynthesis) that might complement N. riversi, although its role as a beneficial symbiont or as a reproductive parasite remains equivocal.

Transcriptome responses to heat and cold stress in prepupae of Trichogramma chilonis

Trichogramma is a useful species that is widely applied in biocontrol. Temperature profoundly affects the commercial application of T. chilonis. Different developmental transcriptomes of prepupae and pupae of T. chilonis under 10, 25, and 40°C were obtained from our previous study. In this study, transcriptomic analysis was further conducted to gain a clear understanding of the molecular changes in the prepupae of T. chilonis under different thermal conditions. A total of 37,295 unigenes were identified from 3 libraries of prepupae of T. chilonis, 17,293 of which were annotated. Differential expression analysis showed that 408 and 108 differentially expressed genes (DEGs) were identified after heat and cold treatment, respectively. Under heat stress, the pathway of protein processing in endoplasmic reticulum was found to be active. Most of the genes involved in this pathway were annotated as lethal (2) essential for life [l(2)efl] and heat shock protein genes (hsps), which were both highly upregulated. Nevertheless, most of the genes involved in another significantly enriched pathway of starch and sucrose metabolism were downregulated, including 1 alpha-glucosidase gene and 2 beta-glucuronidase genes. Under cold stress, no significantly enriched pathway was found, and the significantly enriched GO terms were related to the interaction with host and immune defenses. Together, these results provide us with a comprehensive view of the molecular mechanisms of T. chilonis in response to temperature stresses and will provide new insight into the mass rearing and utilization of T. chilonis.

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.

Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage

Key changes in ecological niche space are often critical to understanding how lineages diversify during adaptive radiations. However, the converse, or understanding why some lineages are depauperate and relictual, is more challenging, as many factors may constrain niche evolution. In the case of the insect order Grylloblattodea, highly conserved thermal breadth is assumed to be closely tied to their relictual status, but has not been formerly tested. Here, we investigate whether evolutionary constraints in the physiological tolerance of temperature can help explain relictualism in this lineage. Using a comparative transcriptomics approach, we investigate gene expression following acute heat and cold stress across members of Grylloblattodea and their sister group, Mantophasmatodea. We additionally examine patterns of protein evolution, to identify candidate genes of positive selection. We demonstrate that cold specialization in Grylloblattodea has been accompanied by the loss of the inducible heat shock response under both acute heat and cold stress. Additionally, there is widespread evidence of selection on protein-coding genes consistent with evolutionary constraints due to cold specialization. This includes positive selection on genes involved in trehalose transport, metabolic function, mitochondrial function, oxygen reduction, oxidative stress, and protein synthesis. These patterns of molecular adaptation suggest that Grylloblattodea have undergone evolutionary trade-offs to survive in cold habitats and should be considered highly vulnerable to climate change. Finally, our transcriptomic data provide a robust backbone phylogeny for generic relationships within Grylloblattodea and Mantophasmatodea. Major phylogenetic splits in each group relate to arid conditions driving biogeographical patterns, with support for a sister-group relationship between North American Grylloblatta and Altai-Sayan Grylloblattella, and a range disjunction in Namibia splitting major clades within Mantophasmatodea.

Transcriptomic and life history responses of the mayfly Neocloeon triangulifer to chronic diel thermal challenge

To better understand the effects of transient thermal stress in an aquatic insect, we first identified static temperatures associated with fitness deficits, and then reared larvae from egg hatch to adulthood under diurnally variable regimens including daily forays into deleterious temperatures. We sampled mature larvae at the coolest and warmest portions of their respective regimens for RNA-seq analysis. Few transcripts (28) were differentially expressed when larvae oscillated between favorable temperatures, while 614 transcripts were differentially expressed when experiencing daily transient thermal stress. Transcripts associated with N-glycan processing were downregulated while those associated with lipid catabolism and chitin turnover were significantly upregulated in heat stressed larvae. An across-regimen comparison of differentially expressed transcripts among organisms sampled at comparable temperatures demonstrated that the effects of daily thermal stress persisted even when larvae were sampled at a more optimal temperature (806 differentially expressed transcripts). The chronically stressed population had reduced expression of transcripts related to ATP synthesis, mitochondrial electron chain functions, gluconeogenesis and glycolytic processes while transcripts associated with cell adhesion, synaptic vesicle transport, regulation of membrane potential and lipid biosynthesis increased. Comparisons of constant vs. variable temperatures revealed that the negative consequences of time spent at stressful temperatures were not offset by more time spent at optimal temperatures.

Phylomitogenomics provides new perspectives on the Euphasmatodea radiation (Insecta: Phasmatodea)

Phasmatodea species diversity lies almost entirely within its suborder Euphasmatodea, which exhibits a pantropical distribution and is considered to derive from a recent and rapid evolutionary radiation. To shed light on Euphasmatodea origins and diversification, we assembled the mitogenomes of 17 species from transcriptomic sequencing data and analysed them along with 22 already available Phasmatodea mitogenomes and 33 mitogenomes representing most of the Polyneoptera lineages. Maximum Likelihood and Bayesian Inference approaches retrieved consistent topologies, both showing the widespread conflict between phylogenetic approaches and traditional systematics. We performed a divergence time analysis leveraging ten fossil specimens representative of most polyneopteran lineages: the time tree obtained supports an older radiation of the clade with respect to previous hypotheses. Euphasmatodea diversification is inferred to have started ~ 187 million years ago, suggesting that the Triassic-Jurassic mass extinction and the breakup of Pangea could have contributed to the process. We also investigated Euphasmatodea mitogenomes patterns of dN, dS and dN/dS ratio throughout our time-tree, trying to characterize the selective regime which may have shaped the clade evolution.

Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand

Phylogeographic concordance, or the sharing of phylogeographic patterns among codistributed species, suggests similar responses to topography or climatic history. While the orientation and timing of breaks between lineages are routinely compared, spatial dynamics within regions occupied by individual lineages provide a second opportunity for comparing responses to past events. In environments with complex topography and glacial history, such as New Zealand's South Island, geographically nested comparisons can identify the processes leading to phylogeographic concordance between and within regional genomic clusters. Here, we used single nucleotide polymorphisms (obtained via ddRADseq) for two codistributed forest beetle species, Agyrtodes labralis (Leiodidae) and Brachynopus scutellaris (Staphylinidae), to evaluate the role of climate change and topography in shaping phylogeographic concordance at two, nested spatial scales: do species diverge over the same geographic barriers, with similar divergence times? And within regions delimited by these breaks, do species share similar spatial dynamics of directional expansion or isolation-by-distance? We found greater congruence of phylogeographic breaks between regions divided by the strongest dispersal barriers (i.e., the Southern Alps). However, these shared breaks were not indicative of shared spatial dynamics within the regions they delimit, and the most similar spatial dynamics between species occurred within regions with the strongest gradients in historical climatic stability. Our results indicate that lack of concordance as traditionally detected by lineage turnover does not rule out the possibility of shared histories, and variation in the presence and type of concordance may provide insights into the different processes shaping phylogeographic patterns across geologically dynamic regions.

Two Lys-vasopressin-like peptides, EFLamide, and other phasmid neuropeptides

Phasmid neuropeptide genes were identified in the genomes of two phasmids, Timema cristinae and Clitarchus hookeri. The two species belong to two sisters groups, the Timematodea and Euphasmatodea respectively. Neuropeptide genes were identified using the BLAST+ program on the genome assemblies and the absence of some neuropeptides was confirmed by the concomitant absence of their G-protein coupled receptors. Both genomes were assembled using short reads and the average coverage of the genome is more than 166 times for both species. This makes it virtually impossible that there would not be a single short read for at least one of the conserved transmembrane regions of a GPCR coded by such a genome. Hence, when not a single read can be found for a specific GPCR, it can be concluded that the particular gene is absent from that species. Most previously identified insect neuropeptides are used by these two species. Of the three arthropod allatostatin C related peptides, only allatostatins CC and CCC are present. Both species lack leucokinin, while sulfakinin and dilp8 signaling is absent from Clitarchus, but present in Timema. Interestingly, whereas Timema has lost a vasopressin-related peptide, the gene coding such a peptide is amplified in the Clitarchus genome. Furthermore, while Clitarchus has a specific tryptopyrokinin gene, Timema does not and in this species tryptopyrokinin is coded only by the pyrokinin and periviscerokinin genes. Finally, both species have genes coding EFLamide and its GPCR; in phasmids these genes codes for one (Clitarchus) or two (Timema) EFLamide paracopies.

New Zealand Tree and Giant Wētā (Orthoptera) Transcriptomics Reveal Divergent Selection Patterns in Metabolic Loci

Exposure to low temperatures requires an organism to overcome physiological challenges. New Zealand wētā belonging to the genera Hemideina and Deinacrida are found across a wide range of thermal environments and therefore subject to varying selective pressures. Here we assess the selection pressures across the wētā phylogeny, with a particular emphasis on identifying genes under positive or diversifying selection. We used RNA-seq to generate transcriptomes for all 18 Deinacrida and Hemideina species. A total of 755 orthologous genes were identified using a bidirectional best-hit approach, with the resulting gene set encompassing a diverse range of functional classes. Analysis of ortholog ratios of synonymous to nonsynonymous amino acid changes found 83 genes that are under positive selection for at least one codon. A wide variety of Gene Ontology terms, enzymes, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways are represented among these genes. In particular, enzymes involved in oxidative phosphorylation, melanin synthesis, and free-radical scavenging are represented, consistent with physiological and metabolic changes that are associated with adaptation to alpine environments. Structural alignment of the transcripts with the most codons under positive selection revealed that the majority of sites are surface residues, and therefore have the potential to influence the thermostability of the enzyme, with the exception of prophenoloxidase where two residues near the active site are under selection. These proteins provide interesting candidates for further analysis of protein evolution.

The Desaturase Gene Family is Crucially Required for Fatty Acid Metabolism and Survival of the Brown Planthopper, Nilaparvata lugens

Desaturases are essentially required for unsaturated fatty acid (UFA) biosynthesis. We identified 10 genes encoding putative desaturases in the transcriptome database of the brown planthopper (BPH), Nilaparvata lugens. These include eight First Desaturase family genes, one cytochrome b5 fused desaturase gene (Nlug-Cytb5r) and one Sphingolipid Desaturase gene (Nlug-ifc). Transcript level profiling revealed significant variation in the expression patterns of these genes across tissues and developmental stages, which occur in a gene-specific manner. Interestingly, their expression was also modulated by the insect food source: the mRNA levels of Nlug-desatC and Nlug-Cytb5r were down-regulated, but the expression level of Nlug-desatA1-b and Nlug-desatA1-c were elevated in the BPH fed on the resistant rice variety Babawee as compared to the non-resistant variety Taichun Native 1 (TN1). Silencing Nlug-desatA1-b, Nlug-desatA1-c, or Nlug-Ifc reduced fatty acid composition and abundance in female BPH 1-d-old-adults compared to controls. Whereas, single knockdown of all ten desaturase genes significantly increased mortality of BPH nymphs compared with controls. Of the ten desaturase genes, knockdown of Nlug-desatA1-b and Nlug-desatA2 caused the highest mortality in BPH (91% and 97%, respectively). Our findings offer a base for expression and functional characterization of newly identified desaturase genes in BPH, and may contribute to RNA interference-based pest management strategies.

Laboratory acclimation to autumn-like conditions induces freeze tolerance in the spring field cricket Gryllus veletis (Orthoptera: Gryllidae)

Many temperate insects encounter temperatures low enough to freeze their body fluids. Remarkably, some insects are freeze-tolerant, surviving this internal ice formation. However, the mechanisms underlying freeze tolerance are not well-understood, in part due to a lack of tractable model organisms. We describe a novel laboratory model to study insect freeze tolerance, the spring field cricket Gryllus veletis (Orthopera: Gryllidae). Following acclimation to six weeks of decreasing temperature and photoperiod, G. veletis become freeze-tolerant, similar to those exposed to natural autumn conditions in London, Ontario, Canada. Acclimated crickets suppress their metabolic rate by c. 33%, and survive freezing for up to one week at -8 °C, and to temperatures as low as -12 °C. Freeze-tolerant G. veletis protect fat body cells from freeze injury in vivo, and fat body tissue from freeze-tolerant cricket survives brief freeze treatments when frozen ex vivo. Freeze-tolerant crickets freeze at c. -6 °C, which may be initiated by accumulation of ice-nucleating agents in hemolymph or gut tissue. Although we hypothesize that control of ice formation facilitates freeze tolerance, initiating ice formation at high subzero temperatures does not confer freeze tolerance on freeze-intolerant nymphs. Acclimation increases hemolymph osmolality from c. 400 to c. 650 mOsm, which may facilitate freeze tolerance by reducing ice content. Hemolymph ion concentrations do not change with acclimation, and we therefore predict that freeze-tolerant G. veletis elevate hemolymph osmolality by accumulating other molecules. Gryllus veletis is easily reared and manipulated in a controlled laboratory environment, and is therefore a suitable candidate for further investigating the mechanisms underlying freeze tolerance.

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.

Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation

The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here, we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species known. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm-adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We also look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, but do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. Finally, we also resequenced three populations of D. montana from across its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.

Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction

BACKGROUND

Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects.

RESULTS

The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified.

CONCLUSIONS

The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.

Differential transcriptome analysis reveals genes related to cold tolerance in seabuckthorn carpenter moth, Eogystia hippophaecolus

Seabuckthorn carpenter moth, Eogystia hippophaecolus (Lepidoptera: Cossidae), is an important pest of sea buckthorn (Hippophae rhamnoides), which is a shrub that has significant ecological and economic value in China. E. hippophaecolus is highly cold tolerant, but limited studies have been conducted to elucidate the molecular mechanisms underlying its cold resistance. Here we sequenced the E. hippophaecolus transcriptome using RNA-Seq technology and performed de novo assembly from the short paired-end reads. We investigated the larval response to cold stress by comparing gene expression profiles between treatments. We obtained 118,034 unigenes, of which 22,161 were annotated with gene descriptions, conserved domains, gene ontology terms, and metabolic pathways. These resulted in 57 GO terms and 193 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. By comparing transcriptome profiles for differential gene expression, we identified many differentially expressed proteins and genes, including heat shock proteins and cuticular proteins which have previously been reported to be involved in cold resistance of insects. This study provides a global transcriptome analysis and an assessment of differential gene expression in E. hippophaecolus under cold stress. We found seven differential expressed genes in common between developmental stages, which were verified with qPCR. Our findings facilitate future genomic studies aimed at improving our understanding of the molecular mechanisms underlying the response of insects to low temperatures.

Transcriptomic analysis to uncover genes affecting cold resistance in the Chinese honey bee (Apis cerana cerana)

The biological activity and geographical distribution of honey bees is strongly temperature-dependent, due to their ectothermic physiology. In China, the endemic Apis cerana cerana exhibits stronger cold hardiness than Western honey bees, making the former species important pollinators of winter-flowering plants. Although studies have examined behavioral and physiological mechanisms underlying cold resistance in bees, data are scarce regarding the exact molecular mechanisms. Here, we investigated gene expression in A. c. cerana under two temperature treatments, using transcriptomic analysis to identify differentially expressed genes (DEGs) and relevant biological processes, respectively. Across the temperature treatments, 501 DEGs were identified. A gene ontology analysis showed that DEGs were enriched in pathways related to sugar and amino acid biosynthesis and metabolism, as well as calcium ion channel activity. Additionally, heat shock proteins, zinc finger proteins, and serine/threonine-protein kinases were differentially expressed between the two treatments. The results of this study provide a general digital expression profile of thermoregulation genes responding to cold hardiness in A. c. cerana. Our data should prove valuable for future research on cold tolerance mechanisms in insects, and may be beneficial in breeding efforts to improve bee hardiness.

Effects of cold-acclimation on gene expression in Fall field cricket (Gryllus pennsylvanicus) ionoregulatory tissues

Background

Cold tolerance is a key determinant of temperate insect distribution and performance. Chill-susceptible insects lose ion and water homeostasis during cold exposure, but prior cold acclimation improves both cold tolerance and defense of homeostasis. The mechanisms underlying these processes are mostly unknown; cold acclimation is thought to enhance ion transport in the cold and/or prevent leak of water and ions. To identify candidate mechanisms of cold tolerance plasticity we generated transcriptomes of ionoregulatory tissues (hindgut and Malpighian tubules) from Gryllus pennsylvanicus crickets and compared gene expression in warm- and cold-acclimated individuals.

Results

We assembled a G. pennsylvanicus transcriptome de novo from 286 million 50-bp reads, yielding 70,037 contigs (~44% of which had putative BLAST identities). We compared the transcriptomes of warm- and cold-acclimated hindguts and Malpighian tubules. Cold acclimation led to a ≥ 2-fold change in the expression of 1493 hindgut genes (733 downregulated, 760 upregulated) and 2008 Malpighian tubule genes (1009 downregulated, 999 upregulated). Cold-acclimated crickets had altered expression of genes putatively associated with ion and water balance, including: a downregulation of V-ATPase and carbonic anhydrase in the Malpighian tubules and an upregulation of Na⁺-K⁺ ATPase in the hindgut. We also observed acclimation-related shifts in the expression of cytoskeletal genes in the hindgut, including actin and actin-anchoring/stabilizing proteins, tubulin, α-actinin, and genes involved in adherens junctions organization. In both tissues, cold acclimation led to differential expression of genes encoding cytochrome P450s, glutathione-S-transferases, apoptosis factors, DNA repair, and heat shock proteins.

Conclusions

This is the first G. pennsylvanicus transcriptome, and our tissue-specific approach yielded new candidate mechanisms of cold tolerance plasticity. Cold acclimation may reduce loss of hemolymph volume in the cold by 1) decreasing primary urine production via reduced expression of carbonic anhydrase and V-ATPase in the Malpighian tubules and 2) by increasing Na⁺ (and therefore water) reabsorption across the hindgut via increase in Na⁺-K⁺ ATPase expression. Cold acclimation may reduce chilling injury by remodeling and stabilizing the hindgut epithelial cytoskeleton and cell-to-cell junctions, and by increasing the expression of genes involved in DNA repair, detoxification, and protein chaperones.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3711-9) contains supplementary material, which is available to authorized users.

CRISPR-induced null alleles show that Frost protects Drosophila melanogaster reproduction after cold exposure

The ability to survive and reproduce after cold exposure is important in all kingdoms of life. However, even in a sophisticated genetic model system like Drosophila melanogaster, few genes have been identified as functioning in cold tolerance. The accumulation of the Frost (Fst) gene transcript increases after cold exposure, making it a good candidate for a gene that has a role in cold tolerance. However, despite extensive RNAi knockdown analysis, no role in cold tolerance has been assigned to Fst. CRISPR is an effective technique for completely knocking down genes, and less likely to produce off-target effects than GAL4-UAS RNAi systems. We have used CRISPR-mediated homologous recombination to generate Fst null alleles, and these Fst alleles uncovered a requirement for FST protein in maintaining female fecundity following cold exposure. However, FST does not have a direct role in survival following cold exposure. FST mRNA accumulates in the Malpighian tubules, and the FST protein is a highly disordered protein with a putative signal peptide for export from the cell. Future work is needed to determine whether FST is exported from the Malpighian tubules and directly interacts with female reproductive tissues post-cold exposure, or if it is required for other repair/recovery functions that indirectly alter energy allocation to reproduction.

Canalization of gene expression is a major signature of regulatory cold adaptation in temperate Drosophila melanogaster

BACKGROUND

Transcriptome analysis may provide means to investigate the underlying genetic causes of shared and divergent phenotypes in different populations and help to identify potential targets of adaptive evolution. Applying RNA sequencing to whole male Drosophila melanogaster from the ancestral tropical African environment and a very recently colonized cold-temperate European environment at both standard laboratory conditions and following a cold shock, we seek to uncover the transcriptional basis of cold adaptation.

RESULTS

In both the ancestral and the derived populations, the predominant characteristic of the cold shock response is the swift and massive upregulation of heat shock proteins and other chaperones. Although we find ~25 % of the genome to be differentially expressed following a cold shock, only relatively few genes (n = 16) are up- or down-regulated in a population-specific way. Intriguingly, 14 of these 16 genes show a greater degree of differential expression in the African population. Likewise, there is an excess of genes with particularly strong cold-induced changes in expression in Africa on a genome-wide scale.

CONCLUSIONS

The analysis of the transcriptional cold shock response most prominently reveals an upregulation of components of a general stress response, which is conserved over many taxa and triggered by a plethora of stressors. Despite the overall response being fairly similar in both populations, there is a definite excess of genes with a strong cold-induced fold-change in Africa. This is consistent with a detrimental deregulation or an overshooting stress response. Thus, the canalization of European gene expression might be responsible for the increased cold tolerance of European flies.

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.

De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction

Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.