HGT is widespread in insects and contributes to male courtship in lepidopterans.

Horizontal gene transfer (HGT) is an important evolutionary force shaping prokaryotic and eukaryotic genomes. HGT-acquired genes have been sporadically reported in insects, a lineage containing >50% of animals. We systematically examined HGT in 218 high-quality genomes of diverse insects and found that they acquired 1,410 genes exhibiting diverse functions, including many not previously reported, via 741 distinct transfers from non-metazoan donors. Lepidopterans had the highest average number of HGT-acquired genes. HGT-acquired genes containing introns exhibited substantially higher expression levels than genes lacking introns, suggesting that intron gains were likely involved in HGT adaptation. Lastly, we used the CRISPR-Cas9 system to edit the prevalent unreported gene LOC105383139, which was transferred into the last common ancestor of moths and butterflies. In diamondback moths, males lacking LOC105383139 courted females significantly less. We conclude that HGT has been a major contributor to insect adaptation.

Compact RNA editors with natural miniature Cas13j nucleases.

Clustered regularly interspaced short palindromic repeats-Cas13 effectors are used for RNA editing but the adeno-associated virus (AAV) packaging limitations because of their big sizes hinder their therapeutic application. Here we report the identification of the Cas13j family, with LepCas13j (529 aa) and ChiCas13j (424 aa) being the smallest and most highly efficient variants for RNA interference. The miniaturized Cas13j proteins enable the development of compact RNA base editors. Chi-RESCUE-S, by fusing dChiCas13j with hADAR2dd, demonstrates high efficiency and specificity in A-to-G and C-to-U conversions. Importantly, this system is compatible with single-AAV packaging without the need for protein sequence truncation. It successfully corrected pathogenic mutations, such as APOC3D65N and SCN9AR896Q, to the wild-type forms. In addition, we developed an optimized system, Chi-RESCUE-S-mini3, which pioneered efficient in vivo C-to-U RNA editing of PCSK9 in mice through single-AAV delivery, resulting in reduced total cholesterol levels. These results highlight the potential of Cas13j to treat human diseases.

The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics.

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring the ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6/15 phylogenomic datasets. Finally, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

How has horizontal gene transfer shaped the evolution of insect genomes?

As the most diverse group of animals on Earth, insects are key organisms in ecosystems. Horizontal gene transfer (HGT) refers to the transfer of genetic material between species by non-reproductive means. HGT is a major evolutionary force in prokaryotic genome evolution, but its importance in different eukaryotic groups, such as insects, has only recently begun to be understood. Genomic data from hundreds of insect species have enabled the detection of large numbers of HGT events and the elucidation of the functions of some of these foreign genes. Although quantification of the extent of HGT in insects broadens our understanding of its role in insect evolution, the scope of its influence and underlying mechanism(s) of its occurrence remain open questions for the field.

A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects.

Neoneuromus ignobilis is an archaic holometabolous aquatic predatory insect. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for adaptive evolution. Here, we provided a high-contiguity, chromosome-level genome assembly of N. ignobilis using high coverage Nanopore and PacBio reads with the Hi-C technique. The final assembly is 480.67 MB in size, containing 12 telomere-ended pseudochromosomes with only 17 gaps. We compared 42 hexapod species genomes including six independent lineages comprising 11 aquatic insects, and found convergent expansions of long wavelength-sensitive and blue-sensitive opsins, thermal stress response TRP channels, and sulfotransferases in aquatic insects, which may be related to their aquatic adaptation. We also detected strong nonrandom signals of convergent amino acid substitutions in aquatic insects. Collectively, our comparative genomic analysis revealed the evidence of molecular convergences in aquatic insects during both gene family evolution and convergent amino acid substitutions.

The mitochondrial genome of Chelonus formosanus (Hymenoptera: Braconidae) with novel gene orders and phylogenetic implications.

Chelonus formosanus Sonan is an important egg-larval parasitoid of noctuid moths and a potential candidate for understanding interactions between host and parasitoid mediated by polydnavirues (PDVs). We sequenced and annotated the mitochondrial genome of C. formosanus, which is 15,466 bp in length and possesses 38 mitochondrial genes. However, unlike most animal mitochondrial genomes, it contains one extra trnF gene. There are five transfer RNA (tRNA) rearrangement events compared with the ancestral gene order, which is a novel rearrangement type in Hymenoptera for all published mitogenomes so far. Phylogenetic trees supported C. formosanus from the subfamily Cheloninae was closely related to the subfamily Cardiochilinae and Microgastrinae.

Comparative mitogenomics and phylogenetics of the stinging wasps (Hymenoptera: Aculeata).

The stinging wasps (Hymenoptera: Aculeata) include diverse groups such as vespid wasps, ants and bees. Phylogenetic relationships among major lineages of stinging wasps have been inferred from molecular and morphological data. However, the genomic features of the mitochondrial genomes and their phylogenetic utility remain to be explored. In this study, we determined 23 mitochondrial genomes from the Aculeata. Four Mutillidae species showed relatively low A + T content compared to other species of the Aculeata (69.7%-77.4%). Eleven out of 44 species, mainly from the Chrysididae and the Pompilidae, showed reversals of GC skews. Gene rearrangements occurred across the species. Patterns of tRNA rearrangement were conserved in some groups, including the Chrysididae, Bethylidae, Pompilidae, Scolioidea and Vespoidea. Rearrangement of protein-coding genes were found in 12 out of 44 species of the Aculeata, including all four species from the Chrysididae, both species from the Bethylidae, one species from the Dryinidae, all three Scolioidea species and two Apoidea species. Phylogenetic inference showed a long branch in species with unusual genomic features, such as in the Mutillidae and Bethylidae. By excluding these species, we found paraphyly of the Chrysidoidea and a sister group relationship between the Formicoidea and Vespoidea. These results improve our understanding of the evolution of mitochondrial genomes in the Aculeata and, in general, the evolution across this subclade.

Intravenous lipid emulsion modifies synaptic transmission in hippocampal CA1 pyramidal neurons after bupivacaine-induced central nervous system toxicity.

Local anesthetics can cause severe toxicity when absorbed systemically. Rapid intravenous administration of lipid emulsion (LE) is the standard of care for severe local anesthetic systemic toxicity which can cause cardiovascular and central nervous system (CNS) injury. The biological mechanism by which LE alleviates CNS toxicity remains unknown and understudied. Previous research has suggested that local anesthetics cause an imbalance of excitatory and inhibitory transmission in the brain. Therefore, this study aimed to observe the effect of LE on glutamate- and GABA-induced currents in CA1 pyramidal neurons after bupivacaine-induced CNS toxicity. We further characterized post-synaptic modifications in these cells to try to elucidate the mechanism by which LE mediates bupivacaine-induced CNS toxicity. Sprague-Dawley rats received intravenous bupivacaine (1 mg kg-1  min-1 ) in either normal saline or LE (or LE without bupivacaine) for 5 min. An acute brain slice preparation and a combination of whole-cell patch clamp techniques and whole-cell recordings were used to characterize action potential properties, miniature excitatory, and inhibitory post-synaptic currents, and post-synaptic modifications of excitatory and inhibitory transmission in CA1 hippocampal pyramidal neurons. The expression level of GABAA receptors were assessed with western blotting, whereas H&E and TUNEL staining were used to assess cytoarchitecture and apoptosis levels respectively. Bupivacaine treatment significantly increased the number of observed action potentials, whereas significantly decreasing rheobase, the first interspike interval (ISI), and hyperpolarization-activated cation currents (Ih) in CA1 pyramidal neurons. LE treatment significantly reduced the frequency of miniature inhibitory post-synaptic currents and enhanced GABA-induced paired pulse ratio with 50 ms interval stimulation in bupivacaine-treated rats. Regulation of GABAA levels is a promising mechanism by which LE may ameliorate CNS toxicity after systemic absorption of bupivacaine.

Systematics, Phylogeny, and Evolution of Braconid Wasps: 30 Years of Progress.

The parasitoid wasp family Braconidae is likely the second-most species-rich family in the animal kingdom. Braconid wasps are widely distributed and often encountered. They constitute one of the principal groups of natural enemies of phytophagous insects, of which many are serious pest species. The enormous biological diversification of braconid wasps has led to many homoplasies, which contributed widely to instabilities in historical classifications. Recent studies using combinations of genetic markers or total mitochondrial genomes allow for better founded groupings and will ultimately lead to a stable classification. We present the current status of the phylogenetics of the Braconidae in a historical perspective and our understanding of the effects on higher classification.

Mitochondrial phylogenomics of the Hymenoptera.

The insect order Hymenoptera presents marvelous morphological and ecological diversity. Higher-level hymenopteran relationships remain controversial, even after recent phylogenomic analyses, as their taxon sampling was limited. To shed light on the origin and diversification of Hymenoptera, in particular the poorly studied Parasitica, we undertook phylogenetic analyses of 40 newly and 43 previously sequenced mitochondrial genomes representing all major clades of Hymenoptera. Various Bayesian inferences using different data partitions and phylogenetic methods recovered similar phylogenetic trees with strong statistical support for almost all nodes. Novel findings of the mitogenomic phylogeny mainly affected the three infraorders Ichneumonomorpha, Proctotrupomorpha and Evaniomorpha, the latter of which was split into three clades. Basal relationships of Parasitica recovered Stephanoidea + (Gasteruptiidae + Aulacidae) as the sister group to Ichneumonomorpha + (Trigonalyoidea + Megalyroidea). This entire clade is sister to Proctotrupomorpha, and Ceraphronoidea + Evaniidae is sister to Aculeata (stinging wasps). Our divergence time analysis indicates that major hymenopteran lineages originated in the Mesozoic. The radiation of early apocritans may have been triggered by the Triassic-Jurassic mass extinction; all extant families were present by the Cretaceous.

Gene arrangement and sequence of mitochondrial genomes yield insights into the phylogeny and evolution of bees and sphecid wasps (Hymenoptera: Apoidea).

The Apoidea represent a large and common superfamily of the Hymenoptera including the bees and sphecid wasps. A robust phylogenetic tree is essential to understanding the diversity, taxonomy and evolution of the Apoidea. In this study, features of apoid mitochondrial genomes were used to reconstruct phylogenetic relationships. Twelve apoid mitochondrial genomes were newly sequenced, representing six families and nine subfamilies. Gene rearrangement events have occurred in all apoid mitochondrial genomes sequenced to date. Sphecid wasps have both tRNA and protein-coding gene rearrangements in 5 of 8 species. In bees, the only rearranged genes are tRNAs; long-tongued bees (Apidae + Megachilidae) are characterized by movement of trnA to the trnI-trnQ-trnM tRNA cluster. Phylogenetic analyses of mitochondrial gene sequences support the known paraphyly of sphecid wasps, with bees nested within this clade. The Ampulicidae is sister to the remaining Apoidea. Crabronidae is paraphyletic, split into Crabronidae s.s. and Philanthidae, with the latter group a sister clade to bees. The monophyletic bees are either classified into two clades, long-tongued bees (Apidae + Megachilidae) and short-tongued bees (Andrenidae + Halictidae + Colletidae + Melitidae), or three groups with the Melitidae sister to the other bees. Our study showed that both gene sequences and arrangements provide information on the phylogeny of apoid families.

Population genetic structure and approximate Bayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) in its native range.

The oriental fruit moth (OFM) Grapholita molesta is one of the most destructive orchard pests. Assumed to be native to China, the moth is now distributed throughout the world. However, the evolutionary history of this moth in its native range remains unknown. In this study, we explored the population genetic structure, dispersal routes and demographic history of the OFM in China and South Korea based on mitochondrial genes and microsatellite loci. The Mantel test indicated a significant correlation between genetic distance and geographical distance in the populations. Bayesian analysis of population genetic structure (baps) identified four nested clusters, while the geneland analysis inferred five genetic groups with spatial discontinuities. Based on the approximate Bayesian computation approach, we found that the OFM was originated from southern China near the Shilin area of Yunnan Province. The early divergence and dispersal of this moth was dated to the Penultimate glaciation of Pleistocene. Further dispersal from southern to northern region of China occurred before the last glacial maximum, while the expansion of population size in the derived populations in northern region of China occurred after the last glacial maximum. Our results indicated that the current distribution and structure of the OFM were complicatedly influenced by climatic and geological events and human activities of cultivation and wide dissemination of peach in ancient China. We provide an example on revealing the origin and dispersal history of an agricultural pest insect in its native range as well as the underlying factors.

Two mitochondrial genomes from the families Bethylidae and Mutillidae: independent rearrangement of protein-coding genes and higher-level phylogeny of the Hymenoptera.

In animal mitochondrial genomes, gene arrangements are usually conserved across major lineages but might be rearranged within derived groups, and might provide valuable phylogenetic characters. Here, we sequenced the mitochondrial genomes of Cephalonomia gallicola (Chrysidoidea: Bethylidae) and Wallacidia oculata (Vespoidea: Mutillidae). In Cephalonomia at least 11 tRNA and 2 protein-coding genes were rearranged, which is the first report of protein-coding gene rearrangements in the Aculeata. In the Hymenoptera, three types of protein-coding gene rearrangement events occur, i.e. reversal, transposition and reverse transposition. Venturia (Ichneumonidae) had the greatest number of common intervals with the ancestral gene arrangement pattern, whereas Philotrypesis (Agaonidae) had the fewest. The most similar rearrangement patterns are shared between Nasonia (Pteromalidae) and Philotrypesis, whereas the most differentiated rearrangements occur between Cotesia (Braconidae) and Philotrypesis. It is clear that protein-coding gene rearrangements in the Hymenoptera are evolutionarily independent across the major lineages but are conserved within groups such as the Chalcidoidea. Phylogenetic analyses supported the sister-group relationship of Orrussoidea and Apocrita, Ichneumonoidea and Aculeata, Vespidae and Apoidea, and the paraphyly of Vespoidea. The Evaniomorpha and phylogenetic relationships within Aculeata remain controversial, with discrepancy between analyses using protein-coding and RNA genes.

The discovery of the genus Spasskia Belokobylskij, 1989 (Hymenoptera: Braconidae) in China, with description of a new species.

The genus Spasskia Belokobylskij, 1989 (Hymenoptera: Braconidae: Helconinae) is reported for the first time from China. Two species, namely Spasskia brevicarinata Yan et Chen sp. n.and Spasskia indica Singh, Belokobylskij et Chauhan, 2005 are described and illustrated. A key to the species of this genus is updated to include the new species.

Redescription of aquatic grass inhabiting Frankliniella zizaniophila (Thripidae: Thripinae) with remarks on its systematic position within the genus Frankliniella (Thysanoptera).

The aquatic grass-inhabiting thrip, Frankliniella zizaniophila (Han & Zhang 1982) (Thripidae: Thripinae), is redescribed and illustrated, and the larvae and the yellow color type of this species are described for the first time. Judging from its unique morphological characters and host plant, the systematic position of this species in Frankliniella is questionable, but until the thrips fauna of Asia is better explored, it seems best to leave this species in Frankliniella, rather than to erect a new monobasic genus.

The genus Polystenus (Hymenoptera: Braconidae: Doryctinae) in China, with descriptions of two new species.

The species of Polystenus Foerster, 1862 (Hymenoptera: Braconidae: Doryctinae) from China are revised, and four species are recognized. Two new species, P. brevitergum sp nov. and P. taiwanus sp nov., are described and illustrated. A key to all species of the genus Polystenus is provided.

Molecular identification of two prophenoloxidase-activating proteases from the hemocytes of Plutella xylostella (Lepidoptera: Plutellidae) and their transcript abundance changes in response to microbial challenges.

The phenoloxidase (PO) activation system plays an important role in insect innate immunity, particularly in wound healing and pathogen defense. A key member of this system is prophenoloxidase-activating protease (PAP), which is the direct activator of prophenoloxidase (proPO). Despite their importance in the insect PO activation system, content of studies is limited. In this article, we identify two complementary DNAs (cDNAs), PxPAPa and PxPAPb, encoding possible PAPs, from immunized larval hemocytes of the diamondback moth, Plutella xylostella (L.), by RACE method. PxPAPa is 1,149-bp long and encodes a 382-residue open reading frame (ORF) with a predicted 17-residue signal peptide, a clip domain, and a Tryp_Spc domain. PxPAPb is 1,650-bp long and encodes a 440-residue ORF with a predicted 20-residue signal peptide, two clip domains, and a Tryp_Spc domain. PxPAPa and PxPAPb have a high sequence similarity to Manduca sexta (L.) PAP1 and PAP3, respectively. We also examined the transcript patterns of PxPAPa, PxPAPb, and pxPAP3, another clip-domain serine protease gene, response to different microbial challenges by using real-time quantitative polymerase chain reaction. The results show that the transcript abundance of PxPAPa is significantly increased by Micrococcus luteus and Escherichia coli but not Candida albicans. PxPAPb is induced only by Mi. luteus, whereas pxPAP3 could be induced by all the microbes in the test, but the transcript patterns of Mi. luteus, E. coli, and C. albicans are completely different. This study provides new insights into the molecular events that occur during the immune response, particularly melanization cascade that is involved in encapsulation and nodulation of pathogen or parasite invaders via hemocytes in host insects.

The grandiculus- and metacarpalis-group of the genus Apanteles Foerster, 1862 (Hymenoptera, Braconidae, Microgastrinae) from China, with descriptions of eight new species.

Two species groups (the grandiculus- and the metacarpalis-group) of genus Apanteles Foerster (Hymenoptera, Braconidae, Microgastrinae) from China are revised and keyed, with eight new species, namely, A. muticiculus Liu & Chen, sp. n., A. parvus Liu & Chen, sp. n. and A. flavicapus Liu & Chen, sp. n. of the grandiculus-group; A. transtergum Liu & Chen, sp. n., A. malleus Liu & Chen, sp. n., A. dumosus Liu & Chen, sp. n. A. cosmopterygivorus Liu & Chen, sp. n. and A. incurvus Liu & Chen, sp. n. of the metacarpalis-group, and two newly recorded species of the metacarpalis-group described and illustrated. Keys to the Chinese species of these two species-groups are provided.

The subgenus Choeras Mason, 1981 of genus Apanteles Foerster, 1862 (Hymenoptera, Braconidae, Microgastrinae) from China, with descriptions of eighteen new species.

The subgenus Choeras Mason, 1981 of genus Apanteles Foerster, 1862 (Hymenoptera, Braconidae, Microgastrinae) from China is revised with 18 new species described and illustrated, and one known species redescribed. A key to the Chinese species of this subgenus is provided.

The genus Ademon Haliday (Hymenoptera: Braconidae: Opiinae) from China, with descriptions of two new species.

The species of Ademon Haliday (Braconidae, Opiiinae) from China are studied. Two new species are described: A. lechrilophodes sp. nov. and A. xuthus sp. nov., and a key to the identification of Old World Ademon is provided.