Comparative Analysis of Mitochondrial Genomes in Gryllidea (Insecta: Orthoptera): Implications for Adaptive Evolution in Ant-Loving Crickets

Chromosome-scale whole genome assembly and annotation of the Jamaican field cricket Gryllus assimilis

Gryllus assimilis, commonly known as Jamaican field cricket, is an edible insect with significant economic value in sustainable food production. Despite its importance, a high-quality reference genome of G. assimilis has not yet been published. Here, we report a chromosome-level reference genome of G. assimilis based on Oxford Nanopore Technologies (ONT) sequencing, Illumina sequencing, and Hi-C technologies. The assembled genome has a total length of 1.60 Gbp with a scaffold N50 of 102 Mbp, and 96.80% of the nucleotides was assigned to 15 chromosome-scale scaffolds. The assembly completeness was validated using BUSCO, achieving 99.5% completeness against the arthropoda database. We predicted 27,645 protein-coding genes, and 825 Mb repetitive elements were annotated in the reference genome. This reference genome of G. assimilis can provide a basis for the subsequent development of genomic resources, offering insights for future functional genomic studies, comparative genomics, and DNA-informed breeding of this species.

Insect Mitochondrial Genomics: A Decade of Progress

The past decade has seen the availability of insect genomic data explode, with mitochondrial (mt) genome data seeing the greatest growth. The widespread adoption of next-generation sequencing has solved many earlier methodological limitations, allowing the routine sequencing of whole mt genomes, including from degraded or museum specimens and in parallel to nuclear genomic projects. The diversity of available taxa now allows finer-scale comparisons between mt and nuclear phylogenomic analyses; high levels of congruence have been found for most orders, with some significant exceptions (e.g., Odonata, Mantodea, Diptera). The evolution of mt gene rearrangements and their association with haplodiploidy have been tested with expanded taxonomic sampling, and earlier proposed trends have been largely supported. Multiple model systems have been developed based on findings unique to insects, including mt genome fragmentation (lice and relatives) and control region duplication (thrips), allowing testing of hypothesized evolutionary drivers of these aberrant genomic phenomena. Finally, emerging research topics consider the contributions of mt genomes to insect speciation and habitat adaption, with very broad potential impacts. Integration between insect mt genomic research and other fields within entomology continues to be our field's greatest opportunity and challenge.

Switching escape strategies in the parasitic ant cricket Myrmecophilus tetramorii

Social parasites employ diverse strategies to deceive and infiltrate their hosts in order to benefit from stable resources. Although escape behaviours are considered an important part of these multipronged strategies, little is known about the repertoire of potential escape behaviours and how they facilitate integration into the host colony. Here, we investigated the escape strategies of the parasitic ant cricket Myrmecophilus tetramorii Ichikawa (Orthoptera: Myrmecophilidae) toward its host and non-host ant workers. We identified two escape strategies with distinct trajectory characteristics by clustering analysis; distancing (defined by high-speed straight movement away from ants for emergency avoidance) and dodging (circular escape movement to get behind ants under low-threat conditions). Interestingly, dodging is dominantly elicited over distancing for host species. Furthermore, our simulations proposed that dodging contributes to efficient foraging while avoiding ants. These results demonstrate that switching to a host-adapted escape strategy facilitates integration of this parasitic cricket into ant nests.

Complete mitochondrial genome sequences of two ground crickets, Dianemobius fascipes nigrofasciatus and Polionemobius taprobanensis (Orthoptera: Grylloidea: trigonidiidae)

The authors sequenced the complete mitochondrial (mt) genomes of the band-legged ground cricket (Dianemobius fascipes nigrofasciatus Matsumura, 1904) and a temperate form of the lawn ground cricket (Polionemobius taprobanensis Walker, 1869), collected in Japan. The length of the mt genome sequences was 15,354 bp in D. fascipes nigrofasciatus and 16,063 bp in P. taprobanensis. Annotation of the mt genome sequences revealed 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The orientation of the genes was the same as in other Grylloidea species, and the order was the same as in other Trigonidiidae species. In our phylogenetic analysis, D. fascipes nigrofasciatus formed a clade with D. fascipes collected in China, and the temperate form of P. taprobanensis formed a clade with P. taprobanensis collected in China. Comparison of the numbers of positions with different amino acid residues encoded by the protein-coding genes implied the separate species status of each member of each of the two pairs of ground crickets. The mt genome sequences of D. fascipes nigrofasciatus and P. taprobanensis will contribute to phylogenetic and taxonomic studies of the Trigonidiidae.

Evolution of mitogenomic gene order in Orthoptera

Mitochondrial gene order has contributed to the elucidation of evolutionary relationships in several animal groups. It generally has found its application as a phylogenetic marker for deep nodes. Yet, in Orthoptera limited research has been performed on the gene order, although the group represents one of the oldest insect orders. We performed a comprehensive study on mitochondrial genome rearrangements (MTRs) within Orthoptera in the context of mitogenomic sequence-based phylogeny. We used 280 published mitogenome sequences from 256 species, including three outgroup species, to reconstruct a molecular phylogeny. Using a heuristic approach, we assigned MTR scenarios to the edges of the phylogenetic tree and reconstructed ancestral gene orders to identify possible synapomorphies in Orthoptera. We found all types of MTRs in our dataset: inversions, transpositions, inverse transpositions, and tandem-duplication/random loss events (TDRL). Most of the suggested MTRs were in single and unrelated species. Out of five MTRs which were unique in subgroups of Orthoptera, we suggest four of them to be synapomorphies; those were in the infraorder Acrididea, in the tribe Holochlorini, in the subfamily Pseudophyllinae, and in the two families Phalangopsidae and Gryllidae or their common ancestor (leading to the relationship ((Phalangopsidae + Gryllidae) + Trigonidiidae)). However, similar MTRs have been found in distant insect lineages. Our findings suggest convergent evolution of specific mitochondrial gene orders in several species, deviant from the evolution of the mitogenome DNA sequence. As most MTRs were detected at terminal nodes, a phylogenetic inference of deeper nodes based on MTRs is not supported. Hence, the marker does not seem to aid resolving the phylogeny of Orthoptera, but adds further evidence for the complex evolution of the whole group, especially at the genetic and genomic levels. The results indicate a high demand for more research on patterns and underlying mechanisms of MTR events in Orthoptera.

De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket (Tachycines meditationis)

Tachycines meditationis (Orthoptera: Rhaphidophoridae: Tachycines) is a widely distributed insect in eastern Asia. This species is common in urban environments, and its unique omnivorous diet may contribute to its success in various habitats. However, molecular studies on the species are scarce. Here, we obtained the first transcriptome sequence of T. meditationis and performed preliminary analyses to test whether the evolution of coding sequences fits the expectations based on the species' ecology. We retrieved 476,495 effective transcripts and annotated 46,593 coding sequences (CDS). We analysed the codon usage and found that directional mutation pressure was the leading cause of codon usage bias in this species. This genome-wide relaxed codon usage pattern in T. meditationis is surprising, given the potentially large population size of this species. Moreover, despite the omnivorous diet, the chemosensory genes of this species do not exhibit codon usage deviating significantly from the genome-level pattern. They also do not seem to experience more gene family expansion than other cave cricket species do. A thorough search for rapidly evolved genes using the dN/dS value showed that genes associated with substance synthesis and metabolic pathways, such as retinol metabolism, aminoacyl-tRNA biosynthesis, and fatty acid metabolism, underwent species-specific positive selection. While some results seem to contradict the species ecology, our transcriptome assembly provides a valuable molecular resource for future studies on camel cricket evolution and molecular genetics for feeding ecology in insects, in general.

The fifth family of the true crickets (Insecta: Orthoptera: Ensifera: Grylloidea), Oecanthidae defin. nov.: phylogenetic relationships and divergence times

Crickets are frequently used as a model in several areas of science, including acoustic communication, behaviour and neurobiology. However, only a few of these studies are placed in an evolutionary framework due to the limited number of phylogenetic hypotheses for true crickets. We present a phylogenetic hypothesis for a newly defined family of crickets, Oecanthidae defin. nov., sister-group of Gryllidae defin. nov. The phylogenetic analyses are based on molecular and morphological data under likelihood and parsimony criteria and molecular data for divergence-times estimation (Bayesian inference). We used 107 terminals from all biogeographic regions and six fossils for the time calibration of the tree. All analyses resulted in Oecanthidae with four subfamilies: Euscyrtinae, Oecanthinae defin. nov., Podoscirtinae defin. nov. and Tafaliscinae defin. nov. Based on our results, we revise the definition and internal classifications of the subfamilies, supertribes and tribes. A new tribe, Phyllogryllini trib. nov. is described. We also update their diagnoses, list the genera of the tribes and list their apomorphies. We provide an identification key for all suprageneric taxa of Oecanthidae, plus all genera of Tafaliscinae. Finally, we discuss the phylogenetic relationships of Oecanthidae, their divergence times, habitat diversity and the importance of ovipositor variation in this clade.

Mitogenomic Comparison of the Mole Crickets Gryllotalpidae with the Phylogenetic Implications (Orthoptera: Ensifera)

Owing to limited molecular data, the phylogenetic position of the family Gryllotalpidae is still controversial in the infraorder Gryllidea. Mitochondrial genome (mitogenome) plays a crucial role in reconstructing phylogenetic relationships and revealing the molecular evolution of insects. However, only four mitogenomes have been reported in Gryllotalpidae to date. Herein, we obtained the first mitogenomes of Gryllotalpa henana Cai & Niu, 1998 and the Chinese G. orientalis Burmeister, 1838, made a detailed comparison of all mitogenomes available in Gryllotalpidae and reconstructed the phylogeny of Gryllidea based on mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. The results show that the complete mitogenome sequences of G. henana (15,504 bp) and G. orientalis (15,497 bp) are conserved, both exhibiting the double-stranded circular structure, typical gene content and the ancestral insect gene arrangement. The complete mitogenome of G.henana exhibits the lowest average AT content ever detected in Gryllotalpidae, and even Gryllidea. The gene nad2 of both species has atypical initiation codon GTG. All tRNAs exhibit typical clover-leaf structure, except for trnS1 lacking the dihydrouridine (DHU) arm. A potential stem-loop structure, containing a (T)_n(TC)₂(T)_n sequence, is detected in the control region of all gryllotalpids investigated and is likely related to the replication initiation of the minority strand. The phylogenetic analyses recover the six families of Gryllidea as Gryllotalpidae + (Myrmecophilidae + (Mogoplistidae + (Trigonidiidae + (Phalangopsidae + Gryllidae)))), similar to the trees based on transcriptomic and mitogenomic data. However, the trees are slightly different from the multilocus phylogenies, which show the sister-group relationship of Gryllotalpidae and Myrmecophilidae. The contradictions between mitogenomic and multilocus trees are briefly discussed.

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.