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.

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.

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.

The discovery of the genus Guaygata Marsh (Hymenoptera, Braconidae, Doryctinae) from China, with description of a new species.

The genus Guaygata Marsh, 1993 is recorded from China for the first time. Two species, i.e. G. mariae (Belokobylskij, 1993) and G. fujianensis sp. nov., are recognized. The new species is fully described and illustrated. A key to Asian species of Guaygata is provided.

Heterospilus Haliday, 1836 (Hymenoptera: Braconidae, Doryctinae) from China with a key to species.

The Chinese species of the genus Heterospilus Haliday, 1836 from the Parasitic Hymenoptera Collection of Zhejiang University were studied and thirty-four species are recognized, including 12 previously described species. Eighteen new species of this genus are described and illustrated: Heterospilus (Heterospilus) alternicoloratus sp. nov., H.(H.) balicyba sp. nov., H.(H.) chui sp. nov., H.(H.) curvisulcus sp. nov., H.(H.) densistriatus sp. nov., H.(H.) fujianensis sp. nov., H.(H.) jianfengensis sp. nov., H.(H.) liui sp. nov., H.(H.) longiventrius sp. nov., H.(H.) nanlingensis sp. nov., H.(H.) parvus sp. nov., H.(H.) prodigiosus sp. nov., H.(H.) punctatus sp. nov., H.(H.) qingliangensis sp. nov., H.(H.) semidepressus sp. nov., H.(H.) setosiscutum sp. nov., H.(H.) setosus sp. nov., and H.(H.) tenuitergum sp. nov. Seven species of Heterospilus are recorded for China for the first time: H. (Eoheterospilus) rubrocinctus (Ashmead, 1905), H.(H.) alboapicalis Belokobylskij, 1994, H.(H.) ater Fischer, 1960, H.(H.) cephi Rohwer, 1925, H.(H.) kerzhneri Belokobylskij et Maetô, 2009, H.(H.) tauricus Telenga, 1941, and H.(H.) tulyensis Belokobylskij, 1994. Two new synonyms are proposed: H. asiaticola Belokobylskij et Maetô, 2009 with H. chinensis Chen et Shi, 2004 and H. gracilis Shi et Chen with H. separatus Fischer, 1960. A key to the Chinese species of Heterospilus is provided.

Regulation of erythropoiesis: emerging concepts and therapeutic implications.

The process of erythropoiesis is complex and involves the transfer of cells from the yolk sac to the fetal hepar and, ultimately, to the bone marrow during embryonic development. Within the bone marrow, erythroid progenitor cells undergo several stages to generate reticulocytes that enter the bloodstream. Erythropoiesis is regulated by various factors, with erythropoietin (EPO) synthesized by the kidney being the promoting factor and hepcidin synthesized by the hepar inhibiting iron mobilization. Transcription factors, such as GATA and KLF, also play a crucial role in erythropoiesis. Disruption of any of these factors can lead to abnormal erythropoiesis, resulting in red cell excess, red cell deficiency, or abnormal morphological function. This review provides a general description of erythropoiesis, as well as its regulation, highlighting the significance of understanding the process for the diagnosis and treatment of various hematological disorders.

The Mitochondrial Genomes of Two Parasitoid Wasps Protapanteles immunis and Parapanteles hyposidrae (Hymenoptera: Braconidae) with Phylogenetic Implications and Novel Gene Rearrangements.

Parapanteles hypsidrae (Wilkinson, 1928) and Protapanteles immunis (Haliday, 1834) are the most important parasitic wasps of Ectropis grisescens Warren and Ectropis obliqua (Prout). We sequenced and annotated the mitochondrial genomes of Pa. hyposidrae and Pr. immunis, which are 17,063 bp and 16,397 bp in length, respectively, and possess 37 mitochondrial genes. We discovered two novel types of gene rearrangement, the local inversion of nad4L in Pa. hyposidrae and the remote inversion of the block cox3-nad3-nad5-nad4 in Pr. immunis, within the mitogenomes of Braconidae. The phylogenetic analysis supported the subfamily Microgastrinae is a monophyletic group, but the tribes Apantelini and Cotesiini within this subfamily are paraphyletic groups.

Chromosome-level genome assembly of Microplitis manilae Ashmead, 1904 (Hymenoptera: Braconidae).

Microplitis manilae Ashmead (Hymenoptera: Braconidae) is an important parasitoid of agricultural pests in lepidopteran species. So far, two extant genome assembles from the genus Microplitis are fragmented. Here, we offered a high-quality genome assembly of M. manilae at the chromosome level with high accuracy and contiguity, assembled by ONT long-read, MGI-SEQ short-read, and Hi-C sequencing methods. The final assembled genome size was 282.85 Mb, with 268.17 Mb assigned to 11 pseudochromosomes. The scaffold N50 length was 25.23 Mb, and the complete BUSCO score was 98.61%. The genome contained 152.37 Mb of repetitive elements, representing 53.87% of the total genome size. We predicted 15,689 protein-coding genes, of which 13,580 genes were annotated functionally. Gene family evolution investigations of M. manilae revealed 615 expanded and 635 contracted gene families. The high-quality genome of M. manilae reported in this paper will be a useful genomic resource for research on parasitoid wasps in the future.

Comparative mitogenomes reveal diverse and novel gene rearrangements in the genus Meteorus (Hymenoptera: Braconidae).

Meteorus Haliday, 1835 is a cosmopolitan genus within Braconidae (Hymenoptera). They are koinobiont endoparasitoids of Coleoptera or Lepidoptera larvae. Only one mitogenome of this genus was available. Here, we sequenced and annotated three mitogenomes of Meteorus species, and found that the tRNA gene rearrangements in these mitogenomes were rich and diverse. Compared with the ancestral organization, only seven tRNAs (trnW, trnY, trnL2, trnH, trnT, trnP and trnV) were conserved and trnG had its own unique location in the four mitogenomes. This dramatic tRNA rearrangement was not observed in mitogenomes of other insect groups before. In addition, the tRNA cluster (trnA-trnR-trnN-trnS1-trnE-trnF) between nad3 and nad5 was rearranged into two patterns, i.e., trnE-trnA-trnR-trnN-trnS1 and trnA-trnR-trnS1-trnE-trnF-trnN. The phylogenetic results showed that the Meteorus species formed a clade within the subfamily Euphorinae, and were close to Zele (Hymenoptera, Braconidae, Euphorinae). In the Meteorus, two clades were reconstructed: M. sp. USNM and Meteorus pulchricornis forming one clade while the remaining two species forming another clade. This phylogenetic relationship also matched the tRNA rearrangement patterns. The diverse and phylogenetic signal of tRNA rearrangements within one genus provided insights into tRNA rearrangements of the mitochondrial genome at genus/species levels in insects.

Evolutionary timescale of chalcidoid wasps inferred from over one hundred mitochondrial genomes.

Chalcidoidea is one of the most biologically diverse groups among Hymenoptera. Members are characterized by extraordinary parasitic lifestyles and extensive host ranges, among which several species attack plants or serve as pollinators. However, higher-level chalcidoid relationships remain controversial. Here, we performed mitochondrial phylogenomic analyses for major clades (18 out of 25 families) of Chalcidoidea based on 139 mitochondrial genomes. The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences. Our phylogenetic results supported the monophyly of 16 families and polyphyly of Aphelinidae and Pteromalidae. Our preferred topology recovered the relationship (Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+ remaining Chalcidoidea)))). The monophyly of Agaonidae and Sycophaginae was rejected, while the gall-associated ((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae)) relationship was supported in most results. A six-gene inversion may be a synapomorphy for most families, whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes. Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea. We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea. Ancestral state reconstruction analyses supported the hypothesis that gall-inducers were mainly derived from parasitoids of gall-inducers, while other gall-inducers were derived from phytophagous groups. Taken together, these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.

Chromosome-level genome assembly of Chouioia cunea Yang, the parasitic wasp of the fall webworm.

Chouioia cunea Yang 1989 is a parasitic wasp of many lepidopteran insects during their pupal stage, and has been successfully used to control pests such as the fall webworm Hyphantria cunea. Here we reported the chromosome-level genome of C. cunea by using short (MGI-SEQ), long (Oxford Nanopore), chromatin-linked (Hi-C) sequencing reads and transcriptomic data, representing the first chromosome-level genome of parasitic wasps of the family Eulophidae. The total assembly length is 171.99 Mb, containing 6 pesudo-chromosomes with a GC content of 36.89% and the scaffold/contig N50 length of 31.70/26.52 Mb. The BUSCO completeness of the assembly was estimated to be 98.7%. A total of 12,258 protein-coding genes (PCGs), 10,547 3'-UTRs, and 10,671 5'-UTRs were annotated. This high-quality genome is an important step toward a better understanding of the genomes of the Eulophidae (Chalcidoidea), and will serve as a valuable resource for analyses of phylogenetic relationships and the evolution of Hymenoptera.

Novel Gene Rearrangements in the Mitochondrial Genomes of Cynipoid Wasps (Hymenoptera: Cynipoidea).

Cynipoidea is a medium-sized superfamily of Hymenoptera with diverse lifestyles. In this study, 16 mitochondrial genomes were newly sequenced, 11 of which were the first obtained mitochondrial genomes in the family Liopteridae and four subfamilies (Anacharitinae, Aspicerinae, Figitinae, and Parnipinae) of Figitidae. All of the newly sequenced mitogenomes have unique rearrangement types within Cynipoidea, whereas some gene patterns are conserved in several groups. nad5-nad4-nad4L-nad6-cytb was remotely inverted and two rRNA genes were translocated to nad3 downstream in Ibaliidae and three subfamilies (Anacharitinae, Eucoilinae, and Parnipinae within Figitidae); two rRNA genes in Aspicerinae, Figitinae, and Liopteridae were remotely inverted to the cytb-nad1 junction; rrnL-rrnS was translocated to the cytb-nad1 junction in Cynipidae. Phylogenetic inference suggested that Figitidae was a polyphyletic group, while the Ibaliidae nested deep within Cynipoidea and was a sister-group to the Figitidae. These results will improve our understanding of the gene rearrangement of the mitogenomes and the phylogenetic relationships in the Cynipoidea.

Mitochondrial Genomes Yield Insights into the Basal Lineages of Ichneumonid Wasps (Hymenoptera: Ichneumonidae).

We obtained four mitochondrial genomes of Odontocolon sp., Xorides funiuensis, Euceros kiushuensis and Euceros serricornis, which represent the first two representatives from subfamily Eucerotinae and Xoridinae (Ichneumonidae), respectively. All of the 4 newly sequenced mitochondrial genomes contain 13 protein-coding genes (PCGs) and most 24 RNA genes. Furthermore, they all have novel tRNA rearrangement patterns comparing with published mitogenomes in Ichneumonidae. For the tRNA cluster trnI-trnQ-trnM, X. funiuensis is shuffled as trnM-trnI-trnQ with trnQ inversed, while Odontocolon sp. with a remote translocation of trnK, shuffling as trnI-trnM-trnQ. E. kiushuensis and E. serricornis shared the same cluster trnQ-trnY-trnW-trnC. Finally, we reconstructed the phylogenetic relationships among the sequenced subfamilies of Ichneumonidae based on nucleotides and amino acids sequences of 13 PCGs in mitochondrial genomes, and the results of both the maximum likelihood and Bayesian inference analyses highly support that Eucerotinae is the basal ichneumonid lineage rather than Xoridinae.

Comparative Mitochondrial Genomics of 104 Darwin Wasps (Hymenoptera: Ichneumonidae) and Its Implication for Phylogeny.

Ichneumonidae is one of the largest families of insects with a mega-diversity of specialized morphological and biological characteristics. We newly sequenced 92 mitochondrial genomes of ichneumonid wasps and found that they have a conserved base composition and a lower evolutionary rate than that of other families of parasitic Hymenoptera. There are 38 types of gene order in the ichneumonid mitochondrial genome, with 30 novel types identified in 104 ichneumonids. We also found that the rearrangement events occur more frequently in Ophioniformes than in Ichneumoniformes and Pimpliformes. Furthermore, the higher Ophioniformes and their relative lineages shared the transposition of trnL2 to trnI-trnQ-trnM tRNA cluster. We confirmed five higher-level groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. The results will improve our understanding of the diversity and evolution of Ichneumonidae.

The Potential of Parapanteles hyposidrae and Protapanteles immunis (Hymenoptera: Braconidae) as Biocontrol Agents for the Tea Grey Geometrid Ectropis grisescens (Lepidoptera).

The tea grey geometrid Ectropis grisescens has long been a significant insect pest of tea plants in China. Two parasitoids, Parapanteles hyposidrae and Protapanteles immunis (Hymenoptera: Braconidae: Microgastrinae), are the most important parasitoids in the larval stage of E. grisescens. Yet, the potential of these two parasitoids for controlling the tea grey geometrid is not known. Here, we studied the parasitism performance of these two parasitoid species on different host densities under different temperatures as well as the interference effect of parasitoid density. The results showed that both parasitoid species, Pa. hyposidrae and Pr. immunis, exhibited a Type II functional response towards the tea grey geometrid E. grisescens at four tested temperatures. With increasing the density of E. grisescens larvae, the number of parasitized larvae increased until a maximum was reached. The highest number of hosts parasitized by Pa. hyposidrae or Pr. immunis reached 14.5 or 14.75 hosts d-1 at 22 °C, respectively. The estimated values of instantaneous searching efficiency (a) and handling time (h) for Pa. hyposidrae or Pr. immunis were 1.420 or 3.621 and 0.04 or 0.053 at 22 °C, respectively. Pr. immunis performed better than Pa. hyposidrae under higher temperatures. The parasitism rate by a single female parasitoid decreased with increasing parasitoid density at different temperatures, resulting in a reduction of searching efficiency. The findings of this study showed that Pr.immunis could be a better effective biocontrol agent than Pa. hyposidrae against the tea grey geometrid.

Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem.

Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera communities on Tianmu Mountain, Zhejiang, China, using DNA metabarcoding technology, and evaluated their dynamic responses to the effects of slope aspect, season, and altitudinal zone. A total of 5,092 operational taxonomic units (OTUs) were discovered and tentatively assigned to 72 dipteran families, including 2 family records new for China and 30 family records new for the locality. Cecidomyiidae, Sciaridae, and Phoridae were the predominant families, representing 53.6% of total OTUs, while 52 families include >95% unidentified and presumed undescribed species. We found that the community structure of Diptera was significantly affected by aspect, seasonality (month) and elevation, with richer diversity harbored in north-facing than south-facing slopes, and seasonality a more profound driver of community structure and diversity than elevation. Overall, massive species diversity of Diptera communities was discovered in this subtropical ecosystem of east China. The huge diversity of potentially undescribed species only revealed by metabarcoding now requires more detailed taxonomic study, as a step toward an evolutionary integration that accumulates information on species' geographic ranges, ecological traits, functional roles, and species interactions, and thus places the local communities in the context of the growing knowledge base of global biodiversity and its response to environmental change.

The chromosome-level genome of Chinese praying mantis Tenodera sinensis (Mantodea: Mantidae) reveals its biology as a predator.

BACKGROUND: The Chinese praying mantis, Tenodera sinensis (Saussure), is a carnivorous insect that preys on a variety of arthropods and small vertebrates, including pest species. Several studies have been conducted to understand its behavior and physiology. However, there is limited knowledge about the genetic information underlying its genome evolution, digestive demands, and predatory behaviors. FINDINGS: Here we have assembled the chromosome-level genome of T. sinensis, representing the first sequenced genome of the family Mantidae, with a genome size of 2.54 Gb and scaffold N50 of 174.78 Mb. Our analyses revealed that 98.6% of BUSCO genes are present, resulting in a well-annotated assembly compared to other insect genomes, containing 25,022 genes. The reconstructed phylogenetic analysis showed the expected topology placing the praying mantis in an appropriate position. Analysis of transposon elements suggested the Gypsy/Dirs family, which belongs to long terminal repeat (LTR) transposons, may be a key factor resulting in the larger genome size. The genome shows expansions in several digestion and detoxification associated gene families, including trypsin and glycosyl hydrolase (GH) genes, ATP-binding cassette (ABC) transporter, and carboxylesterase (CarE), reflecting the possible genomic basis of digestive demands. Furthermore, we have found 1 ultraviolet-sensitive opsin and 2 long-wavelength-sensitive (LWS) opsins, emphasizing the core role of LWS opsins in regulating predatory behaviors. CONCLUSIONS: The high-quality genome assembly of the praying mantis provides a valuable repository for studying the evolutionary patterns of the mantis genomes and the gene expression profiles of insect predators.

The mitochondrial genome of Telenomus remus (Hymenoptera: Platygastridae).

Telenomus remus Nixon, 1937 is an important parasitoid of lepidopterans. We sequenced the mitochondrial genome of T. remus, 15,500 bp in size, and possessed all 37 typical mitochondrial genes. A few tRNAs show gene arrangements compared with the ancestral gene order, mainly involving in the four tRNA clusters (E-C-Y-Q-I-A, D-K, N-F-S1-R, and M-V). The nucleotide sequences of 13 protein-coding genes of this sequence and another seven species from Platygastridae were used for phylogenetic analysis by MrBayes, with two species from Cynipoidea as an outgroup. The topology demonstrated that T. remus was most closely related to Telenomus sp.