Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans

Genome size and chromosome number are critical metrics for accurate genome assembly assessment in Eukaryota

The number of genome assemblies has rapidly increased in recent history, with NCBI databases reaching over 41,000 eukaryotic genome assemblies across about 2,300 species. Increases in read length and improvements in assembly algorithms have led to increased contiguity and larger genome assemblies. While this number of assemblies is impressive, only about a third of these assemblies have corresponding genome size estimations for their respective species on publicly available databases. In this paper, genome assemblies are assessed regarding their total size compared to their respective publicly available genome size estimations. These deviations in size are assessed related to genome size, kingdom, sequencing platform, and standard assembly metrics, such as N50 and BUSCO values. A large proportion of assemblies deviate from their estimated genome size by more than 10%, with increasing deviations in size with increased genome size, suggesting nonprotein coding and structural DNA may be to blame. Modest differences in performance of sequencing platforms are noted as well. While standard metrics of genome assessment are more likely to indicate an assembly approaching the estimated genome size, much of the variation in this deviation in size is not explained with these raw metrics. A new, proportional N50 metric is proposed, in which N50 values are made relative to the average chromosome size of each species. This new metric has a stronger relationship with complete genome assemblies and, due to its proportional nature, allows for a more direct comparison across assemblies for genomes with variation in sizes and architectures.

Repetitive element expansions contribute to genome size gigantism in Pamphagidae: A comparative study (Orthoptera, Acridoidea)

Pamphagidae is a family of Acridoidea that inhabits the desert steppes of Eurasia and Africa. This study employed flow cytometry to estimate the genome size of eight species in the Pamphagidae. The results indicate that the genome size of the eight species ranged from 13.88 pg to 14.66 pg, with an average of 14.26 pg. This is the largest average genome size recorded for the Orthoptera families, as well as for the entire Insecta. Furthermore, the study explored the role of repetitive sequences in the genome, including their evolutionary dynamics and activity, using low-coverage next-generation sequencing data. The genome is composed of 14 different types of repetitive sequences, which collectively make up between 59.9% and 68.17% of the total genome. The Pamphagidae family displays high levels of transposable element (TE) activity, with the number of TEs increasing and accumulating since the family's emergence. The study found that the types of repetitive sequences contributing to the TE outburst events are similar across species. Additionally, the study identified unique repetitive elements for each species. The differences in repetitive sequences among the eight Pamphagidae species correspond to their phylogenetic relationships. The study sheds new light on genome gigantism in the Pamphagidae and provides insight into the correlation between genome size and repetitive sequences within the family.

Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation

Transposable elements (TEs) are a major component of eukaryotic genomes and are present in almost all eukaryotic organisms. TEs are highly dynamic between and within species, which significantly affects the general applicability of the TE databases. Orthoptera is the only known group in the class Insecta with a significantly enlarged genome (0.93-21.48 Gb). When analyzing the large genome using the existing TE public database, the efficiency of TE annotation is not satisfactory. To address this limitation, it becomes imperative to continually update the available TE resource library and the need for an Orthoptera-specific library as more insect genomes are publicly available. Here, we used the complete genome data of 12 Orthoptera species to de novo annotate TEs, then manually re-annotate the unclassified TEs to construct a non-redundant Orthoptera-specific TE library: Orthoptera-TElib. Orthoptera-TElib contains 24,021 TE entries including the re-annotated results of 13,964 unknown TEs. The naming of TE entries in Orthoptera-TElib adopts the same naming as RepeatMasker and Dfam and is encoded as the three-level form of "level1/level2-level3". Orthoptera-TElib can be directly used as an input reference database and is compatible with mainstream repetitive sequence analysis software such as RepeatMasker and dnaPipeTE. When analyzing TEs of Orthoptera species, Orthoptera-TElib performs better TE annotation as compared to Dfam and Repbase regardless of using low-coverage sequencing or genome assembly data. The most improved TE annotation result is Angaracris rhodopa, which has increased from 7.89% of the genome to 53.28%. Finally, Orthoptera-TElib is stored in Sqlite3 for the convenience of data updates and user access.

Variation in temperature of peak trait performance constrains adaptation of arthropod populations to climatic warming

The capacity of arthropod populations to adapt to long-term climatic warming is currently uncertain. Here we combine theory and extensive data to show that the rate of their thermal adaptation to climatic warming will be constrained in two fundamental ways. First, the rate of thermal adaptation of an arthropod population is predicted to be limited by changes in the temperatures at which the performance of four key life-history traits can peak, in a specific order of declining importance: juvenile development, adult fecundity, juvenile mortality and adult mortality. Second, directional thermal adaptation is constrained due to differences in the temperature of the peak performance of these four traits, with these differences expected to persist because of energetic allocation and life-history trade-offs. We compile a new global dataset of 61 diverse arthropod species which provides strong empirical evidence to support these predictions, demonstrating that contemporary populations have indeed evolved under these constraints. Our results provide a basis for using relatively feasible trait measurements to predict the adaptive capacity of diverse arthropod populations to geographic temperature gradients, as well as ongoing and future climatic warming.

Effects of Temperature Adaptation on the Metabolism and Physiological Properties of Sturgeon Fish Larvae Cell Line

This study investigated how Atlantic sturgeon cells respond to elevated temperatures, shedding light on the potential impacts of climate change on fish. Atlantic sturgeon (Acipenser oxyrinchus), an IUCN (International Union for Conservation of Nature) Red List species and evolutionarily related to paleonisiform species, may have considerable physiological adaptability, suggesting that this species may be able to cope with changing climatic conditions and higher temperatures. To test this hypothesis, the AOXlar7y cell line was examined at 20 °C (control) and at elevated temperatures of 25 °C and 28 °C. Parameters including proliferation, vitality, morphology, and gene expressions related to proliferation, stemness, and stress were evaluated. Additionally, to achieve a comprehensive understanding of cellular changes, mitochondrial and metabolic activities were assessed using Seahorse XF96. AOXlar7y cells adapted to 28 °C exhibited enhanced mitochondrial adaptability, plasticity, heightened cell proliferation, and increased hsp70 expression. Increased baseline respiration indicated elevated ATP demand, which is potentially linked to higher cell proliferation and heat stress defense. Cells at 28 °C also displayed elevated reserve respiration capacity, suggesting adaptation to energy demands. At 25 °C, AOXlar7y cells showed no changes in basal respiration or mitochondrial capacity, suggesting unchanged ATP demand compared to cells cultivated at 20 °C. Proliferation and glycolytic response to energy requirements were diminished, implying a connection between glycolysis inhibition and proliferation suppression. These research results indicate sturgeon cells are capable of withstanding and adapting to an 8 °C temperature increase. This cellular analysis lays a foundation for future studies aimed at a deeper understanding of fish cell physiological adaptations, which will contribute to a better knowledge of environmental threats facing Atlantic sturgeon and fish populations amid climate change.

Comparative analysis of mitogenomes among three species of grasshoppers (Orthoptera: Acridoidea: Gomphocerinae) and their phylogenetic implications

Whole mitochondrial genomes have been widely used in phylogenetic analysis, population genetics and biogeography studies. This study sequenced and characterized three complete mitochondrial genomes (Dasyhippus peipingensis, Myrmeleotettix palpalis, Aeropedellus prominemarginis) and determined their phylogenetic position in Acrididae. The length of the mitochondrial genomes ranged from 15,621-15,629 bp and composed of 13 PCGs, 2 rRNA, 22 tRNA genes and an AT control region. The arrangement and structure of the mitochondrial genomes were similar to those of other invertebrates. Comparative genomics revealed that the three mitochondrial genomes were highly conserved in terms of gene size, structure, and codon usage, all PCGs were purified selections with an ATN start codon and a TAN stop codon. All tRNAs could be folded into the typical clover-leaf structure, except tRNA Ser (AGN) that lacked a dihydrouridine (DHU) arm. Phylogenetic analysis based on 13 PCGs of 34 Acrididae species and seven outgroup species revealed that differences in the shape of antennae within the family Acrididae should be given less weight as a taxonomic character for higher-level classification. Moreover, the divergence time estimates indicates that in Gomphocerinae, the species with clubbed antennae were formed within the nearest 18 Mya, and Pacris xizangensis is more ancient.

Ecological factors and parity mode correlate with genome size variation in squamate reptiles

BACKGROUND

Evidence of correlation between genome size, the nuclear haploid DNA content of a cell, environmental factors and life-history traits have been reported in many animal species. Genome size, however, spans over three orders of magnitude across taxa and such a correlation does not seem to follow a universal pattern. In squamate reptiles, the second most species-rich order of vertebrates, there are currently no studies investigating drivers of genome size variability. We run a series of phylogenetic generalized least-squares models on 227 species of squamates to test for possible relationships between genome size and ecological factors including latitudinal distribution, bioclimatic variables and microhabitat use. We also tested whether genome size variation can be associated with parity mode, a highly variable life history trait in this order of reptiles.

RESULTS

The best-fitting model showed that the interaction between microhabitat use and parity mode mainly accounted for genome size variation. Larger genome sizes were found in live-bearing species that live in rock/sand ecosystems and in egg-laying arboreal taxa. On the other hand, smaller genomes were found in fossorial live-bearing species.

CONCLUSIONS

Environmental factors and species parity mode appear to be among the main parameters explaining genome size variation in squamates. Our results suggest that genome size may favour adaptation of some species to certain environments or could otherwise result from the interaction between environmental factors and parity mode. Integration of genome size and genome sequencing data could help understand the role of differential genome content in the evolutionary process of genome size variation in squamates.

Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling

The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.

DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species

BACKGROUND

Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools.

RESULTS

The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera.

CONCLUSIONS

This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.

Contrasting Phylogeographic Patterns of Mitochondrial and Genome-Wide Variation in the Groundwater Amphipod Crangonyx islandicus That Survived the Ice Age in Iceland

The analysis of phylogeographic patterns has often been based on mitochondrial DNA variation, but recent analyses dealing with nuclear DNA have in some instances revealed mito-nuclear discordances and complex evolutionary histories. These enigmatic scenarios, which may involve stochastic lineage sorting, ancestral hybridization, past dispersal and secondary contacts, are increasingly scrutinized with a new generation of genomic tools such as RADseq, which also poses additional analytical challenges. Here, we revisited the previously inconclusive phylogeographic history, showing the mito-nuclear discordance of an endemic groundwater amphipod from Iceland, Crangonyx islandicus, which is the only metazoan known to have survived the Pleistocene beneath the glaciers. Previous studies based on three DNA markers documented a mitochondrial scenario with the main divergence occurring between populations in northern Iceland and an ITS scenario with the main divergence between the south and north. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to clarify this mito-nuclear discordance by applying several statistical methods while estimating the sensitivity to different analytical approaches (data-type, differentiation indices and base call uncertainty). A majority of nuclear markers and methods support the ITS divergence. Nevertheless, a more complex scenario emerges, possibly involving introgression led by male-biased dispersal among northern locations or mitochondrial capture, which may have been further strengthened by natural selection.

Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development

Genome size varies ∼100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, join the lungfish in having the largest vertebrate genomes-3 to 40 times that of humans-as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.

Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism

Background

Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. However, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of TE invasion by imposing small-RNA-mediated silencing. Here we compare the TE activity of two grasshopper species with different genome sizes in Acrididae (Locusta migratoria manilensis♀1C = 6.60 pg, Angaracris rhodopa♀1C = 16.36 pg) to ascertain the influence of piRNAs.

Results

We discovered that repetitive sequences accounted for 74.56% of the genome in A. rhodopa, more than 56.83% in L. migratoria, and the large-genome grasshopper contained a higher TEs proportions. The comparative analysis revealed that 41 TEs (copy number > 500) were shared in both species. The two species exhibited distinct “landscapes” of TE divergence. The TEs outbreaks in the small-genome grasshopper occurred at more ancient times, while the large-genome grasshopper maintains active transposition events in the recent past. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. We found that TE transcript abundance was higher in the large-genome grasshopper and the TE-derived piRNAs abundance was lower than in the small-genome grasshopper. In addition, we found that the piRNA methylase HENMT, which is underexpressed in the large-genome grasshopper, impedes the piRNA silencing to a lower level.

Conclusions

Our study revealed that the abundance of piRNAs is lower in the gigantic genome grasshopper than in the small genome grasshopper. In addition, the key gene HENMT in the piRNA biogenesis pathway (Ping-Pong cycle) in the gigantic genome grasshopper is underexpressed. We hypothesize that low-level piRNA silencing unbalances the original positive correlation between TEs and piRNAs, and triggers TEs to proliferate out of control, which may be one of the reasons for the gigantism of grasshopper genomes.

Experimental Crossing Confirms Reproductive Isolation between Cryptic Species within Eulimnogammarus verrucosus (Crustacea: Amphipoda) from Lake Baikal

Ancient lakes are known speciation hotspots. One of the most speciose groups in the ancient Lake Baikal are gammaroid amphipods (Crustacea: Amphipoda: Gammaroidea). There are over 350 morphological species and subspecies of amphipods in Baikal, but the extent of cryptic variation is still unclear. One of the most common species in the littoral zone of the lake, Eulimnogammarus verrucosus (Gerstfeldt, 1858), was recently found to comprise at least three (pseudo)cryptic species based on molecular data. Here, we further explored these species by analyzing their mitogenome-based phylogeny, genome sizes with flow cytometry, and their reproductive compatibility. We found divergent times of millions of years and different genome sizes in the three species (6.1, 6.9 and 8 pg), further confirming their genetic separation. Experimental crossing of the western and southern species, which are morphologically indistinguishable and have adjacent ranges, showed their separation with a post-zygotic reproductive barrier, as hybrid embryos stopped developing roughly at the onset of gastrulation. Thus, the previously applied barcoding approach effectively indicated the separate biological species within E. verrucosus. These results provide new data for investigating genome evolution and highlight the need for precise tracking of the sample origin in any studies in this morphospecies.

Ecological, physiological and life-history traits correlate with genome sizes in decapod crustaceans

Crustaceans are characterized by some of the most variable genome sizes among animals. Significant relationships between genome size and specific eco-physiological and morphological features have been described in many crustacean taxa, such as Amphipoda, Ostracoda, Cladocera, and Copepoda. A consistent pattern of genome size variation is yet to be found, however, in one of the most specious order of crustaceans, the Decapoda. We investigated how genome size is related to selected eco-physiological and life-history traits in species belonging to this order. We analyzed the respiratory, excretory, and developmental adaptations of 179 decapod species inhabiting shallow marine, deep marine, freshwater, intertidal, and terrestrial habitats. Our results show that the genome size is significantly larger in decapods that have a direct development. Moreover, in Anomura, Astacidea, and Brachyura we found larger genome sizes in species (i) living in freshwater habitats, (ii) using gills as a strictly water-breathing organs, and (iii) presenting a direct development. While species that (i) live in shallow waters, and intertidal and terrestrial habitats, (ii) have some degrees of air-breathing adaptations, namely gills that can exchange oxygen with air if wet or branchiostegal lungs, and (iii) possess an indirect or extended development are characterized by significantly smaller genomes. Our analyses show that developmental complexity affects genome size in decapods, and that multiple eco-physiological and life-history traits correlate with genome size in Anomura, Astacidea, and Brachyura.

Transposons and Non-coding Regions Drive the Intrafamily Differences of Genome Size in Insects

Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand the specific evolutionary factors that determine GS in insects, we examined flow cytometry-based published GS data from 1,326 insect species, spanning 700 genera, 155 families, and 21 orders. Model fitting showed that GS generally followed an Ornstein–Uhlenbeck adaptive evolutionary model in Insecta overall. Ancestral reconstruction indicated a likely GS of 1,069 Mb, suggesting that most insect clades appeared to undergo massive genome expansions or contractions. Quantification of genomic components in 56 species from nine families in four insect orders revealed that the proliferation of transposable elements contributed to high variation in GS between close species, such as within Coleoptera. This study sheds lights on the pattern of GS variation in insects and provides a better understanding of insect GS evolution.

•

The most comprehensive variation pattern of insects genome size (GS) to date

•

GS evolution of the Insecta was reflected by the adaptive Ornstein–Uhlenbeck model

•

Ancestral state of insect GS was estimated to be ∼1 Gb

•

Intrafamily GS variations were driven by recent transpositions and non-coding regions

Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis

Crustaceans constitute a species-rich and ecologically important animal group, and their circulating blood cells (hemocytes) are of critical importance in immunity as key players in pathogen recognition, phagocytosis, melanization, and antimicrobial defense. To gain a better understanding of the immune responses to different pathogens, it is crucial that we identify different hemocyte subpopulations with different functions and gain a better understanding of how these cells are formed. Here, we performed single-cell RNA sequencing of isolated hematopoietic tissue (HPT) cells and hemocytes from the crayfish Pacifastacus leniusculus to identify hitherto undescribed hemocyte types in the circulation and show that the circulating cells are more diversified than previously recognized. In addition, we discovered cell populations in the HPT with clear precursor characteristics as well as cells involved in iron homeostasis, representing a previously undiscovered cell type. These findings may improve our understanding of hematopoietic stem cell regulation in crustaceans and other animals.

•

Single-cell RNA sequencing of hematopoietic cell types reveals new cell types

•

One cell type contains iron homeostasis-associated transcripts

•

Hemocytes and hematopoietic cells differ in their transcript profiles

•

Prophenoloxidase is only expressed in hemocytes

Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad

Genomic resources for amphibians are still hugely under-represented in vertebrate genomic research, despite being a group of major interest for ecology, evolution and conservation. Amphibians constitute a highly threatened group of vertebrates, present a vast diversity in reproductive modes, are extremely diverse in morphology, occupy most ecoregions of the world, and present the widest range in genome sizes of any major group of vertebrates. We combined Illumina, Nanopore and Hi-C sequencing technologies to assemble a chromosome-level genome sequence for an anuran with a moderate genome size (assembly span 3.09 Gb); Pelobates cultripes, the western spadefoot toad. The genome has an N50 length of 330 Mb with 98.6% of the total sequence length assembled into 14 super scaffolds, and 87.7% complete BUSCO genes. We use published transcriptomic data to provide annotations, identifying 32,684 protein-coding genes. We also reconstruct the P. cultripes phylome and identify 2,527 gene expansions. We contribute the first draft of the genome of the western spadefoot toad, P. cultripes. This species represents a relatively basal lineage in the anuran tree with an interesting ecology and a high degree of developmental plasticity, and thus is an important resource for amphibian genomic research.

Genome size evolution in the diverse insect order Trichoptera

Background

Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages.

Results

We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments).

Conclusion

Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.

Dissecting cricket genomes for the advancement of entomology and entomophagy

Significant advances in biophysical methods such as next-generation sequencing technologies have now opened the way to conduct evolutionary and applied research based on the genomic information of greatly diverse insects. Crickets belonging to Orthoptera (Insecta: Polyneoptera), one of the most flourishing groups of insects, have contributed to the development of multiple scientific fields including developmental biology and neuroscience and have been attractive targets in evolutionary ecology for their diverse ecological niches. In addition, crickets have recently gained recognition as food and feed. However, the genomic information underlying their biological basis and application research toward breeding is currently underrepresented. In this review, we summarize the progress of genomics of crickets. First, we outline the phylogenetic position of crickets in insects and then introduce recent studies on cricket genomics and transcriptomics in a variety of fields. Furthermore, we present findings from our analysis of polyneopteran genomes, with a particular focus on their large genome sizes, chromosome number, and repetitive sequences. Finally, how the cricket genome can be beneficial to the food industry is discussed. This review is expected to enhance greater recognition of how important the cricket genomes are to the multiple biological fields and how basic research based on cricket genome information can contribute to tackling global food security.

Interacting Effects of Cell Size and Temperature on Gene Expression, Growth, Development and Swimming Performance in Larval Zebrafish

Cell size may be important in understanding the thermal biology of ectotherms, as the regulation and consequences of cell size appear to be temperature dependent. Using a recently developed model system of triploid zebrafish (which have around 1.5-fold larger cells than their diploid counterparts) we examine the effects of cell size on gene expression, growth, development and swimming performance in zebrafish larvae at different temperatures. Both temperature and ploidy affected the expression of genes related to metabolic processes (citrate synthase and lactate dehydrogenase), growth and swimming performance. Temperature also increased development rate, but there was no effect of ploidy level. We did find interactive effects between ploidy and temperature for gene expression, body size and swimming performance, confirming that the consequences of cell size are temperature dependent. Triploids with larger cells performed best at cool conditions, while diploids performed better at warmer conditions. These results suggest different selection pressures on ectotherms and their cell size in cold and warm habitats.

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes

To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.

The Evolutionary Patterns of Genome Size in Ensifera (Insecta: Orthoptera)

Genomic size variation has long been a focus for biologists. However, due to the lack of genome size data, the mechanisms behind this variation and the biological significance of insect genome size are rarely studied systematically. The detailed taxonomy and phylogeny of the Ensifera, as well as the extensive documentation concerning their morphological, ecological, behavioral, and distributional characteristics, make them a strong model for studying the important scientific problem of genome size variation. However, data on the genome size of Ensifera are rather sparse. In our study, we used flow cytometry to determine the genome size of 32 species of Ensifera, the smallest one being only 1C = 0.952 pg with the largest species up to 1C = 19.135 pg, representing a 20-fold range. This provides a broader blueprint for the genome size variation of Orthoptera than was previously available. We also completed the assembly of nine mitochondrial genomes and combined mitochondrial genome data from public databases to construct phylogenetic trees containing 32 species of Ensifera and three outgroups. Based on these inferred phylogenetic trees, we detected the phylogenetic signal of genome size variation in Ensifera and found that it was strong in both males and females. Phylogenetic comparative analyses revealed that there were no correlations between genome size and body size or flight ability in Tettigoniidae. Reconstruction of ancestral genome size revealed that the genome size of Ensifera evolved in a complex pattern, in which the genome size of the grylloid clade tended to decrease while that of the non-grylloid clade expanded significantly albeit with fluctuations. However, the evolutionary mechanisms underlying variation of genome size in Ensifera are still unknown.

Lineage-level divergence of copepod glycerol transporters and the emergence of isoform-specific trafficking regulation

Transmembrane conductance of small uncharged solutes such as glycerol typically occurs through aquaglyceroporins (Glps), which are commonly encoded by multiple genes in metazoan organisms. To date, however, little is known concerning the evolution of Glps in Crustacea or what forces might underly such apparent gene redundancy. Here, we show that Glp evolution in Crustacea is highly divergent, ranging from single copy genes in species of pedunculate barnacles, tadpole shrimps, isopods, amphipods and decapods to up to 10 copies in diplostracan water fleas although with monophyletic origins in each lineage. By contrast the evolution of Glps in Copepoda appears to be polyphyletic, with surprisingly high rates of gene duplication occurring in a genera- and species-specific manner. Based upon functional experiments on the Glps from a parasitic copepod (Lepeophtheirus salmonis), we show that such lineage-level gene duplication and splice variation is coupled with a high rate of neofunctionalization. In the case of L. salmonis, splice variation of a given gene resulted in tissue- or sex-specific expression of the channels, with each variant evolving unique sites for protein kinase C (PKC)- or protein kinase A (PKA)-regulation of intracellular membrane trafficking. The combined data sets thus reveal that mutations favouring a high fidelity control of intracellular trafficking regulation can be a selection force for the evolution and retention of multiple Glps in copepods.

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.

Divergent nucleic acid allocation in juvenile insects of different metamorphosis modes

Nucleic acids help clarify variation in species richness of insects having different metamorphosis modes, a biological conundrum. Here we analyse nucleic acid contents of 639 specimens of aquatic insects collected from four high mountain streams of Sierra Nevada in southern Spain to test whether the allocation to RNA or DNA content differs during ontogeny between juvenile insects undergoing direct (hemimetabolous) or indirect (holometabolous) metamorphosis. The results show that RNA content as a function of body mass was negatively correlated to insect body length in four out of six and three out of six of the holometabolan and hemimetabolan taxa, respectively. Although no significant differences in RNA content were found between holometabolans and hemimetabolans, the significant interaction between body length and metamorphosis mode for RNA and RNA:DNA indicates a strong ontogenetic component to RNA allocation. In addition, our finding of lower DNA content in holometabolans relative to hemimetabolans agree with the analysis of empirical genome data in aquatic and terrestrial insects, and extend to this class of arthropods the “growth rate-genome size-nutrient limitation” hypothesis that differences in allocation between RNA and DNA may reflect fundamental evolutionary trade-off of life-history strategies associated with high growth rates (and RNA content) in holometabolans at the expense of diminished genome sizes.

Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem

The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.

Shrinking body sizes in response to warming: explanations for the temperature-size rule with special emphasis on the role of oxygen

Body size is central to ecology at levels ranging from organismal fecundity to the functioning of communities and ecosystems. Understanding temperature-induced variations in body size is therefore of fundamental and applied interest, yet thermal responses of body size remain poorly understood. Temperature-size (T-S) responses tend to be negative (e.g. smaller body size at maturity when reared under warmer conditions), which has been termed the temperature-size rule (TSR). Explanations emphasize either physiological mechanisms (e.g. limitation of oxygen or other resources and temperature-dependent resource allocation) or the adaptive value of either a large body size (e.g. to increase fecundity) or a short development time (e.g. in response to increased mortality in warm conditions). Oxygen limitation could act as a proximate factor, but we suggest it more likely constitutes a selective pressure to reduce body size in the warm: risks of oxygen limitation will be reduced as a consequence of evolution eliminating genotypes more prone to oxygen limitation. Thus, T-S responses can be explained by the 'Ghost of Oxygen-limitation Past', whereby the resulting (evolved) T-S responses safeguard sufficient oxygen provisioning under warmer conditions, reflecting the balance between oxygen supply and demands experienced by ancestors. T-S responses vary considerably across species, but some of this variation is predictable. Body-size reductions with warming are stronger in aquatic taxa than in terrestrial taxa. We discuss whether larger aquatic taxa may especially face greater risks of oxygen limitation as they grow, which may be manifested at the cellular level, the level of the gills and the whole-organism level. In contrast to aquatic species, terrestrial ectotherms may be less prone to oxygen limitation and prioritize early maturity over large size, likely because overwintering is more challenging, with concomitant stronger end-of season time constraints. Mechanisms related to time constraints and oxygen limitation are not mutually exclusive explanations for the TSR. Rather, these and other mechanisms may operate in tandem. But their relative importance may vary depending on the ecology and physiology of the species in question, explaining not only the general tendency of negative T-S responses but also variation in T-S responses among animals differing in mode of respiration (e.g. water breathers versus air breathers), genome size, voltinism and thermally associated behaviour (e.g. heliotherms).

The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition

The mechanisms and processes driving change and variation in the genome size (GS) are not well known, and only a small set of ant species has been studied. Ants are an ecologically successful insect group present in most distinct ecosystems worldwide. Considering their wide distribution and ecological plasticity in different environmental contexts, we aimed to expand GS estimation within Formicidae to examine distribution patterns and variation in GS and base composition and to reconstruct the ancestral state of this character in an attempt to elucidate the generalized pattern of genomic expansions. Genome size estimates were generated for 99 ant species, including new GS estimates for 91 species of ants, and the mean GS of Formicidae was found to be 0.38 pg. The AT/GC ratio was 62.40/37.60. The phylogenetic reconstruction suggested an ancestral GS of 0.38 pg according to the Bayesian inference/Markov chain Monte Carlo method and 0.37 pg according to maximum likelihood and parsimony methods; significant differences in GS were observed between the subfamilies sampled. Our results suggest that the evolution of GS in Formicidae occurred through loss and accumulation of non-coding regions, mainly transposable elements, and occasionally by whole genome duplication. However, further studies are needed to verify whether these changes in DNA content are related to colonization processes, as suggested at the intraspecific level.

Genome Size of 17 Species From Caelifera (Orthoptera) and Determination of Internal Standards With Very Large Genome Size in Insecta

Comparative studies of insect genome size show that Orthoptera is a unique group of Insecta with a significantly enlarged genome. To determine a suitable internal standard for a large genome and to compare the effects of different internal standards on estimates of genome size, we used four internal standards to estimate nuclear DNA content in nine insect species with large genomes. The results showed that the combination of two internal standards, Locusta migratoria (♂1C = 6.20 pg, ♀1C = 6.60 pg) and Periplaneta americana♂ (1C = 3.41 pg), was suitable for estimating large genome of Caelifera by flow cytometry. Using these two internal standards, we estimated the genome sizes of 17 species of Caelifera (12 genera in Acrididae, 2 genera in Pamphagidae, 1 genus in Pyrgomorphidae) using flow cytometry. Genomes ranged from 6.57 pg (Shirakiacris shirakii) to 18.64 pg (Bryodemella holdereri), the largest described in insects to date. These species showed significant genomic dimorphism based on sex: females had a 0.56 pg larger genome than males on average, which might be due to the sex chromosome determinism mechanism of X0(♂)/XX(♀). To test the results obtained by flow cytometry, we used k-mers of Illumina sequencing data to gauge the C-value of Calliptamus abbreviatus and Haplotropis brunneriana. The results of the two methods are slightly different. Genomes were estimated to be about 0.28 and 0.26 pg smaller, respectively, than the flow cytometry values. Furthermore, we also reconstructed the evolutionary relationships of these taxa and discuss the genome size evolution in a phylogenetic framework.

The whale shark genome reveals how genomic and physiological properties scale with body size

The endangered whale shark (Rhincodon typus) is the largest fish on Earth and a long-lived member of the ancient Elasmobranchii clade. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 83 animals and yeast. We examined the scaling relationships between body size, temperature, metabolic rates, and genomic features and found both general correlations across the animal kingdom and features specific to the whale shark genome. Among animals, increased lifespan is positively correlated to body size and metabolic rate. Several genomic traits also significantly correlated with body size, including intron and gene length. Our large-scale comparative genomic analysis uncovered general features of metazoan genome architecture: Guanine and cytosine (GC) content and codon adaptation index are negatively correlated, and neural connectivity genes are longer than average genes in most genomes. Focusing on the whale shark genome, we identified multiple features that significantly correlate with lifespan. Among these were very long gene length, due to introns being highly enriched in repetitive elements such as CR1-like long interspersed nuclear elements, and considerably longer neural genes of several types, including connectivity, activity, and neurodegeneration genes. The whale shark genome also has the second slowest evolutionary rate observed in vertebrates to date. Our comparative genomics approach uncovered multiple genetic features associated with body size, metabolic rate, and lifespan and showed that the whale shark is a promising model for studies of neural architecture and lifespan.

New Biological Morphogenetic Methods for Evolutionary Design of Robot Bodies

We present some currently unused morphogenetic mechanisms from evolutionary biology and guidelines for transfer to evolutionary robotics. (1) DNA patterns providing mutation of mutability, lead to canalization of evolvable bauplans, via kin selection. (2) Morphogenetic mechanisms (i) Epigenetic cell lines provide functional cell types, and identification of cell descent. (ii) Local anatomical coordinates based on diffusion of morphogens, facilitate evolvable genetic parameterizations of complex phenotypes (iii) Remodeling in response to mechanical forces facilitates robust production of well-integrated phenotypes of greater complexity than the genome. An approach is proposed for the tractable application of mutation-of-mutability and morphogenetic mechanisms in evolutionary robotics. The purpose of these methods, is to facilitate production of robot mechanisms of the subtlety, efficiency, and efficacy of the musculoskeletal and dermal systems of animals.

Triploidy in zebrafish larvae: Effects on gene expression, cell size and cell number, growth, development and swimming performance

There is renewed interest in the regulation and consequences of cell size adaptations in studies on understanding the ecophysiology of ectotherms. Here we test if induction of triploidy, which increases cell size in zebrafish (Danio rerio), makes for a good model system to study consequences of cell size. Ideally, diploid and triploid zebrafish should differ in cell size, but should otherwise be comparable in order to be suitable as a model. We induced triploidy by cold shock and compared diploid and triploid zebrafish larvae under standard rearing conditions for differences in genome size, cell size and cell number, development, growth and swimming performance and expression of housekeeping genes and hsp70.1. Triploid zebrafish have larger but fewer cells, and the increase in cell size matched the increase in genome size (+ 50%). Under standard conditions, patterns in gene expression, ontogenetic development and larval growth were near identical between triploids and diploids. However, under demanding conditions (i.e. the maximum swimming velocity during an escape response), triploid larvae performed poorer than their diploid counterparts, especially after repeated stimuli to induce swimming. This result is consistent with the idea that larger cells have less capacity to generate energy, which becomes manifest during repeated physical exertion resulting in increased fatigue. Triploidy induction in zebrafish appears a valid method to increase specifically cell size and this provides a model system to test for consequences of cell size adaptation for the energy budget and swimming performance of this ectothermic vertebrate.

Genome size and lifestyle in gnesiotrochan rotifers

Gnesiotrochan rotifers display a variety of life styles ranging from taxa with free-swimming larval and sessile adult stages to those with motile adult stages and colonial habits. Several explanations for the C- value enigma posits that genome size is correlated with lifestyle. To investigate this, 13 gnesiotrochan species representing nine genera were measured by flow cytometry. Genome sizes (1C) within Gnesiotrocha ranged from 0.05 pg (Hexarthra mira and Hexarthra fennica) to 0.25 pg (Sinantherina ariprepes). Genome sizes varied within genera and species; e.g., H. fennica (El Huérfano, Mexico) was estimated to be 15% larger than that of H. mira and H. fennica (Keystone Wetland, TX, USA). Gnesiotrochan genome sizes are similar to those reported within Ploima, which range from 0.06 pg (Brachionus rotundiformis, B. dimidiatus) to 0.46 pg (B. asplanchnoidis). Within Gnesiotrocha, genome size was found to be significantly smaller in sessile versus motile species as well as in solitary versus colonial species. To account for phylogenetic background, Linear Mixed Models with hierarchical taxonomic ranks showed that there is a taxonomic component underlying genome size. This study provides the first estimates of genome size within the superorder, providing a baseline for genomic and evolutionary studies within the group.

De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate

Amphibians are highly vulnerable and diverse vertebrates for which we still have modest genomic resources. Amphibian larvae are key components of continental wetlands, where they have strong influences on energy fluxes, nutrient cycling, and community structure. Amphibian larvae are highly sensitive to environmental conditions and can often alter their physiology, behavior and even morphology in response to the local conditions experienced, although we still know relatively little about the transcriptomic changes that enable such plasticity. Here we contribute the larval transcriptomes of two spadefoot toad species with divergent developmental rates and degree of developmental plasticity in response to pond drying.

Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients

Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi, Aphaenogaster floridana, Aphaenogaster fulva, Aphaenogaster miamiana, Aphaenogaster picea, and Aphaenogaster rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8-396.0 Mb) and flow cytometry estimates (210.7-690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes.

Genome Size Reversely Correlates With Host Plant Range in Helicoverpa Species

In organisms with very low percentages of transposable elements (TEs), genome size may positively or negatively correlate with host range, depending on whether host adaptation or host modification is the main route to host generalism. To test if this holds true for insect herbivores with greater percentages of TEs, we conducted flow cytometry to measure the endopolyploidy levels and C-values of the host modification (salivary gland and mandibular gland in head), host adaptation (midgut), and host use-independent tissues (male gonad, hemolymph, and Malpighian tubules) of the generalist Helicoverpa armigera and the head of its older specialist sister H. assulta. Larval salivary gland displayed a consecutive chain of endopolyploidy particles from 8Cx to higher than 32Cx and larval head and midgut had endopolyploidy nuclei clusters of 16Cx and 32Cx, whereas larval male gonad, hemolymph, and Malpighian tubules possessed no endopolyploidy nuclei of higher than 8Cx. The estimated genome size of the Solanaceae plant specialist H. assulta is 430 Mb, significantly larger than that of its older generalist sister Heliothis virescens (408 Mb) and those of its two generalist descendants H. armigera (394 Mb) and H. zea (363 Mb). These data not only reveal a negative correlation between host plant range and genome size in this terminal lineage, but also imply that Helicoverpa species appear to depend more on host modification than on host adaptation to achieve polyphagy.

A study of the role of vision in the foraging behaviour of the pyrrhocorid bug Antilochus conquebertii (Insecta; Hemiptera; Pyrrhocoridae)

Our study aims to describe (1) external morphology of the compound eye of Antilochus conquebertii, (2) postembryonic changes involving the eye's shape and size and (3) behaviour of the animal with respect to the organization of the compound eye. With each moult of the insect, the structural units of the compound eye increase in size as well as the number, resulting in an overall increase in eye size. The resolution of the adult eye is better than the young one. The adult possesses UV and polarization sensitivity in its eye. Parallel to the changes of the eye the behaviour of the adult animal changes, rendering it increasingly nocturnal and less active in under illuminated conditions. The current study describes the eye and its functional relationship with the behaviour of the animal at the nymphal and adult developmental stage.

The transcriptome of the marine calanoid copepod Temora longicornis under heat stress and recovery

Understanding the impacts of global change in zooplankton communities is crucial, as alterations in the zooplankton communities can affect entire marine ecosystems. Despite the economic and ecological importance of the calanoid copepod Temora longicornis in the Belgian part of the North Sea, molecular data is still very limited for this species. Using HiSeq Illumina sequencing, we sequenced the whole transcriptome of T. longicornis, after being exposed to realistic temperatures of 14 and 17 °C. After both an acute (1 day) and a more sustained (5 days) thermal exposure to 17 °C, we investigated gene expression differences with animals exposed to 14 °C, which may be critical for the thermal acclimation and resilience of this copepod species. We also studied the possibility of a short term stress recovery of a heat shock. A total of 179,569 transcripts were yielded, of which 44,985 putative ORF transcripts were identified. These transcripts were subsequently annotated into roughly 22,000 genes based on known sequences using Gene Ontology (GO) and KEGG databases. Temora only showed a mild response to both the temperature and the duration of the exposure. We found that the expression of 27 transcripts varied significantly with an increase in temperature of 3 °C, of which eight transcripts were differentially expressed after acute exposure only. Gene set enrichment analysis revealed that, overall, T. longicornis was more impacted by a sustained thermal exposure, rather than an immediate (acute) exposure, with two times as many enriched GO terms in the sustained treatment. We also identified several general stress responses independent of exposure time, such as modified protein synthesis, energy mobilisation, cuticle and chaperone proteins. Finally, we highlighted candidate genes of a possible recovery from heat exposure, identifying similar terms as those enriched in the heat treatments, i.e. related to for example energy metabolism, cuticle genes and extracellular matrix. The data presented in this study provides the first transcriptome available for T. longicornis which can be used for future genomic studies.

Genome size estimation of brackishwater fishes and penaeid shrimps by flow cytometry

Flow cytometry was used for estimating the genome size of five brackishwater finfish and four shrimp species. The genome size for Lutjanus argentimaculatus was 0.95 ± 0.10 and 0.79 ± 0.01 pg for Scatophagus argus. The genome sizes for Chanos chanos (0.72 ± 0.01 pg), Etroplus suratensis (1.71 ± 0.16 pg) and Liza macrolepis (0.87 ± 0.02 pg) which are important aquaculture species are reported for the first time in this study. The phylogenetic tree constructed using sixty-seven sequence accessions of cytochrome c oxidase subunit 1 (COI) gene of Lates calcarifer revealed two separate clades. The Indian Lates calcarifer species with estimated genome size of 0.44 ± 0.02 pg belonged to a clade different than that of South East Asia and Australia reported to have larger genome size. The genome size for the four major species of genus Penaeus (Penaeus monodon, Penaeus indicus, Penaeus vannamei and Penaeus japonicus) were found in similar range. The genome size of female shrimps ranged from 2.91 ± 0.03 pg (P. monodon) to 2.14 ± 0.02 pg (P. japonicus). In male shrimps, the genome size ranged from 2.86 ± 0.06 pg (P. monodon) to 2.19 ± 0.02 pg (P. indicus). Significant difference was observed in the genome size between male and female shrimp of all species except in P. monodon. The highest relative difference of 12.78% was observed in the genome size between the either sex in P. indicus. The interspecific relative difference of 30.59% in genome size was highest between the male shrimps of P. monodon and P. indicus and 35.98% between the female shrimps of P. monodon and P. japonicus. The stored gills and pleopod tissues could be successfully used up to 3 weeks to estimate the genome size in shrimps.

Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans

Despite the major role of genome size for physiology, ecology, and evolution, there is still mixed evidence with regard to proximate and ultimate drivers. The main causes of large genome size are proliferation of noncoding elements and/or duplication events. The relative role and interplay between these proximate causes and the evolutionary patterns shaped by phylogeny, life history traits or environment are largely unknown for the arthropods. Genome size shows a tremendous variability in this group, and it has a major impact on a range of fitness-related parameters such as growth, metabolism, life history traits, and for many species also body size. In this study, we compared genome size in two major arthropod groups, insects and crustaceans, and related this to phylogenetic patterns and parameters affecting ambient temperature (latitude, depth, or altitude), insect developmental mode, as well as crustacean body size and habitat, for species where data were available. For the insects, the genome size is clearly phylogeny-dependent, reflecting primarily their life history and mode of development, while for crustaceans there was a weaker association between genome size and phylogeny, suggesting life cycle strategies and habitat as more important determinants. Maximum observed latitude and depth, and their combined effect, showed positive, and possibly phylogenetic independent, correlations with genome size for crustaceans. This study illustrate the striking difference in genome sizes both between and within these two major groups of arthropods, and that while living in the cold with low developmental rates may promote large genomes in marine crustaceans, there is a multitude of proximate and ultimate drivers of genome size.