Identification of candidate chemosensory genes in Bactrocera cucurbitae based on antennal transcriptome analysis.

The melon fly, Bactrocera cucurbitae (Coquillett) (Tephritidae: Diptera), is an invasive pest that poses a significant threat to agriculture in Africa and other regions. Flies are known to use their olfactory systems to recognise environmental chemical cues. However, the molecular components of the chemosensory system of B. cucurbitae are poorly characterised. To address this knowledge gap, we have used next-generation sequencing to analyse the antenna transcriptomes of sexually immature B. cucurbitae adults. The results have identified 160 potential chemosensory genes, including 35 odourant-binding proteins (OBPs), one chemosensory protein (CSP), three sensory neuron membrane proteins (SNMPs), 70 odourant receptors (ORs), 30 ionotropic receptors (IRs), and 21 gustatory receptors (GRs). Quantitative real-time polymerase chain reaction quantitative polymerase chain reaction was used to validate the results by assessing the expression profiles of 25 ORs and 15 OBPs. Notably, high expression levels for BcucOBP5/9/10/18/21/23/26 were observed in both the female and male antennae. Furthermore, BcucOROrco/6/7/9/13/15/25/27/28/42/62 exhibited biased expression in the male antennae, whereas BcucOR55 showed biased expression in the female antennae. This comprehensive investigation provides valuable insights into insect olfaction at the molecular level and will, thus, help to facilitate the development of enhanced pest management strategies in the future.

Electroantennographic and Behavioral Responses of the Melon fly, Zeugodacus cucurbitae (Coquillett), to Volatile Compounds of Ridge Gourd, Luffa acutangular L.

The melon fly, Zeugodacus cucurbitae (Coquillett), is a major invasive pest, widely distributed in the Asia-Pacific region and some parts of Africa. Melon fly attractants could improve the effectiveness of current pest management measures. Previous studies have shown that some host fruits are attractive to melon flies but few have investigated the chemical compounds responsible for their attraction. In this study, we aimed to identify the volatile compounds from Luffa acutangula L that attract Z. cucurbitae. In headspace trapping, chemical profiling identified 19 compounds from ridge gourds, with 1-pentadecene being the major component. EAG results revealed that seven compounds elicited antennal responses in Z. cucurbitae, and significant differences in antennal responses between male and female Z. cucurbitae adults were recorded to p-xylene, alpha-pinene, and 1-octadecene. Behavioral experiments demonstrated that the EAG-active compounds methyl isovalerate and methyl myristate had either attractive or repellent effects on Z. cucurbitae at different concentrations, and 1-octadecene attracted Z. cucurbitae. Our findings provide a theoretical basis producing repellents or attractants for effective Integrated Pest Management of Z. cucurbitae.

Effect of host shift on the gut microbes of Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae).

Background: Gut microbes play an important role in the adaptation of insects. Polyphagous insects usually undergo changes in gut microbiota after host shift. The Bactrocera cucurbitae have a wide range of hosts, but the dynamic of gut microorganisms during host shift have not been thoroughly investigated. To understand the role of gut microbes in insect adaptation, it is necessary to study the dynamics of insect gut microorganisms during host transfer. Methods: Using Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae) and its four hosts as study subjects, we investigated the dynamics of gut microbes during host transfer and the effects of different hosts on the gut microbial composition of B. cucurbitae. Results: The results showed that the Chao1 index of B. cucurbitae decreased significantly during host transfer, and the intestinal microorganisms were significantly affected by the original host, host, and generations. Furthermore, predicated changes in the abundance of secondary metabolite pathways after host transfer suggested that microorganisms may play an important role in the degradation of secondary metabolites, among which Providencia and Morganella have important functions in the gut of B. cucurbitae. Conclusion: This implied that microorganisms play a function in the host transfer process of B. cucurbitae and may be an important cofactor in the adaptation of B. cucurbitae to different hosts and environments, providing new research ideas for the future control of B. cucurbitae.

Chromosome-level genome assembly of an agricultural pest Zeugodacus tau (Diptera: Tephritidae).

The fruit fly Zeugodacus tau (Diptera: Tephritidae) is a major pest of melons and other cucurbits in Southeast Asia. In this study, we used Illumina, Nanopore, and Hi-C sequencing technologies to assemble a reference genome of Z. tau at the chromosomal level. The assembled genome was 421.79 Mb and consisted of six chromosomes (one X-chromosome + five autosomes). The contig N50 was 4.23 Mb. We identified 20,922 protein-coding genes, of which 17,251 (82.45%) were functionally annotated. Additionally, we found 247 rRNAs, 435 tRNAs, 67 small nuclear RNAs, and 829 small RNAs in the genome. Repetitive elements accounted for 55.30 Mb (13.15%) of the genome. This high-quality genome assembly is valuable for evolutionary and genetic studies of Z. tau and its relative species.

Complete Mitochondrial Genome Characterization of Schrankia costaestrigalis (Insecta: Erebidae: Hypenodinae) and Its Phylogenetic Implication.

The pinion-streaked snout Schrankia costaestrigalis is a new potato pest that has recently been recorded in China. In this study, we analyzed the complete mitochondrial genome of S. costaestrigalis. The results revealed the mitogenome (GenBank: OQ181231) to occur as a circular DNA molecule of 16,376 bp with 51.001% AT content, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 control region. Notably, the PCGs exhibited typical ATN (Met) start codons, including cox1, which deviated from the usual CGA start codon observed in other lepidopteran mitogenomes, and followed the conventional TAN stop codons. The 22 tRNA genes demonstrated the ability to form a cloverleaf structure, with the exception of trnS1-NCU, which lacked the DHU arm present in other Erebidae mitogenomes. Additionally, conserved motifs like "ATAGA + poly-T (19 bp) stretch" and five microsatellite-like elements (TA) were identified in the AT-rich region. The phylogenetic trees revealed that the Hypenodinae subfamily forms an independent lineage closely related to Erebinae and Catocalinae. The comprehensive mitogenome of S. costaestrigalis will greatly enhance future studies focused on the molecular classification and phylogenetic understanding of the Hypenodinae subfamily within the larger family Erebidae.

Rapid response of midgut bacteria in Bactrocera tau (Walker) (Diptera: Tephritidae) to lambda-cyhalothrin- and spinosad-induced stress.

In recent decades, the increasingly widespread application of chemical pesticides has exacerbated the emergence of insecticide resistance among insect pests. In this study, we examined the rapid response of bacteria in the midgut of the fruit fly Bactrocera tau (Walker) (Diptera: Tephritidae) to stress induced by the insecticides lambda-cyhalothrin and spinosad by analyzing the bacterial community structure and diversity in the midguts of 4-day-old B. tau. The results revealed that 4-day-old B. tau females were more resistant to lambda-cyhalothrin and spinosad than their 4-day-old male counterparts. Alpha- and beta-diversity analyses revealed no significant differences between male and female B. tau with respect to the diversity and richness of gut bacteria in response to the same treatments. In response to treatment with lambda-cyhalothrin and spinosad at lethal concentration 50 (LC50), we detected significant changes in the structure and diversity of the bacterial community in the midguts of both male and female B. tau. Particularly among the dominant bacterial genera, there were decreases in the relative abundances of Citrobacter, Enterobacter, Klebsiella, and Pectobacterium. Increases were observed in the relative abundances of Dysgonomonas, Erwinia, and Providencia. Our findings provide a theoretical basis for gaining a better understanding of the relationships between midgut bacteria and the insecticide resistance of B. tau.

Feeding on rapid cold hardening Ambrosia artemisiifolia enhances cold tolerance of Ophraella communa.

Low temperatures greatly influence newly introduced species, and increased cold tolerance can facilitate their establishment in new environments. The invasive alien species Ambrosia artemisiifolia is distributed at high latitudes and altitudes, where it suffers more from cold stress than it would at low latitudes or altitudes. Whether cold stress influences the accumulation of cryoprotectants and cold tolerance in A. artemisiifolia, and further influences the cold tolerance of its biological control agent, Ophraella communa, through feeding remain unknown. We investigated the levels of cryoprotectants and metabolic changes in A. artemisiifolia. We found that the level of total sugar, trehalose, proline, and other cold responsible metabolites increased in A. artemisiifolia after rapid cold-hardening (RCH) treatment, when compared to normal plants. These indicated that RCH treatment could improve the cold-hardiness of A. artemisiifolia. We then investigated the levels of cryoprotectants and metabolic changes in O. communa. We found that O. communa fed on RCH-treated A. artemisiifolia had higher levels of total sugar, trehalose, proline, glycerol, lipid, lower water content, lower super-cooling point, and increased cold tolerance compared to O. communa fed on normal A. artemisiifolia. This suggested that O. communa fed on cold-hardened A. artemisiifolia could increase its cold tolerance. Results showed a trophic transmission in insect cold tolerance. Our study enriches the theoretical basis for the co-evolution of cold tolerance in invasive and herbivorous insects.

Single-cell landscape of primary central nervous system diffuse large B-cell lymphoma.

Understanding tumor heterogeneity and immune infiltrates within the tumor-immune microenvironment (TIME) is essential for the innovation of immunotherapies. Here, combining single-cell transcriptomics and chromatin accessibility sequencing, we profile the intratumor heterogeneity of malignant cells and immune properties of the TIME in primary central nervous system diffuse large B-cell lymphoma (PCNS DLBCL) patients. We demonstrate diverse malignant programs related to tumor-promoting pathways, cell cycle and B-cell immune response. By integrating data from independent systemic DLBCL and follicular lymphoma cohorts, we reveal a prosurvival program with aberrantly elevated RNA splicing activity that is uniquely associated with PCNS DLBCL. Moreover, a plasmablast-like program that recurs across PCNS/activated B-cell DLBCL predicts a worse prognosis. In addition, clonally expanded CD8 T cells in PCNS DLBCL undergo a transition from a pre-exhaustion-like state to exhaustion, and exhibit higher exhaustion signature scores than systemic DLBCL. Thus, our study sheds light on potential reasons for the poor prognosis of PCNS DLBCL patients, which will facilitate the development of targeted therapy.

The carboxypeptidase B and carbonic anhydrase genes play a reproductive regulatory role during multiple matings in Ophraella communa.

Seminal fluid proteins (SFPs) are key factors in sexual reproduction and are transferred to females during mating with sperm. SFPs have a nutritional value because they protect and activate sperm storage and release to optimize fecundity. Multiple matings promote ovipositioning in several insect species. Therefore, insects may obtain more SFP through multiple matings to maximize reproduction, but this process has not yet been clearly confirmed. Here, the relationship between multiple matings and the SFPs in Ophraella communa (Coleoptera: Chrysomelidae), a biological control agent of the common ragweed Ambrosia artemisiifolia (Asterales: Asteraceae), was studied. Multiple matings significantly increased female fecundity and ovary egg deposition. Carboxypeptidase B (OcCpb) and carbonic anhydrase (OcCa) genes were identified as putative SFP genes in O. communa and they showed strong male-biased expression. Additionally, OcCpb and OcCa expression was upregulated in the bursa copulatrix of mating females compared to that in virgin females, but their expression gradually declined after copulation. Furthermore, OcCpb and OcCa knockdown in males led to a decrease in insect fecundity compared to that in the control. The reproductive tract of females mated with dsRNA-treated males was dissected and observed and, notably, the ovaries produced significantly fewer eggs. These data suggest that OcCpb and OcCa play regulatory roles during multiple matings in O. communa.

Complete mitochondrial genome and phylogenetic analysis of Mastax latefasciata Liebke 1931 (Insecta: Coleoptera: Carabidae).

The genus Mastax Fischer von Waldheim 1827 belongs to the family Carabidae. Specimens of adult Mastax latefasciata Liebke, 1931 were collected from Yajì Hill, Huáihuà City, Húnán Province, China. The complete mitochondrial genome (GenBank accession number ON674050.1) of M. latefasciata was sequenced, annotated, and characterized. The results showed that it was a circular DNA molecule of 16,735 bp with 81.07% AT content and comprised 13 protein-coding genes (PCG), 22 tRNA genes, 2 rRNA genes, and 1 control region. The PCGs were initiated using typical ATN (Met) and TTG (Met) start codons and terminated using typical TAN stop codons. The phylogenetic position of Mastax within the Carabidae was first evaluated using complete mitogenomes, and the results showed that it was close to Cicindela anchoralis and Manticora tibialis.

Complete Mitogenome and Phylogenetic Analyses of Galerita orientalis Schmidt-Goebel, 1846 (Insecta: Coleoptera: Carabidae: Galeritini).

The genus Galerita Fabricius, 1801 belongs to the tribe Galeritini of the family Carabidae. In this study, the complete mitochondrial genome (GenBank: ON920164.1) of G. orientalis is newly sequenced, annotated, characterized, and composed of 37 typical genes, and one control region. Mitogenome is a circular DNA molecule of 16,137 bp with a 78.79% AT content. All 13 protein-coding genes are initiated using a typical ATN (Met) as the start codon, except for nad1, which has a TTG as the start codon, and are terminated using a typical TAN stop codon. Twenty-two tRNAs could fold into a typical cloverleaf structure, including trnS1-GCU, which lacks the DHU stem observed in other mitogenomes of the subfamily Harpalinae. Both rrnS and rrnL contain many helices. A conserved poly-T stretch (19 bp) and seven tandem repeats are observed in the control region, and a phylogenetic analysis indicated that the genus Galerita is an independent lineage. The complete mitogenome of G. orientalis will contribute to further studies on the molecular basis of the classification and phylogeny of Harpalinae, and even Carabidae.

Single-cell transcriptome profiling and chromatin accessibility reveal an exhausted regulatory CD4+ T cell subset in systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease, and CD4+ T cells are known to promote SLE development. Here, we explore heterogeneities in the CD4+ T cell regulome and their associations with SLE pathogenesis by performing assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and single-cell transcriptome sequencing (single-cell RNA sequencing [scRNA-seq]) of peripheral CD4+ T cells from 72 SLE patients and 30 healthy controls. Chromatin accessibility signatures of CD4+ T cells are correlated with disease severity. Further, we generate 34,176 single-cell transcriptomes of healthy and SLE CD4+ T cells and reveal transcriptional dysfunction of regulatory T (Treg) cells, identifying two Treg subpopulations, among which the CCR7lowCD74hi Treg subgroup features type I interferon-induced functional exhaustion in SLE patients. These transcriptome-level findings for SLE Tregs are mirrored in trends from the ATAC-seq data. Our study establishes a rich empirical foundation for understanding SLE and uncovers previously unknown contributions of Treg with exhaustion-like properties to SLE pathogenesis.

Comparative mitogenome analysis reveals mitochondrial genome characteristics in eight strains of Beauveria.

Despite the significant progress that has been made in the genome sequencing of Beauveria species, mitochondrial genome (mitogenome) used to examine genetic diversity within fungal populations. Complete mitogenomes of Beauveria species can be easily sequenced and assembled using various sequencing techniques. However, since mitogenome annotations are mainly derived from similar species comparison and software prediction, and are not supported by RNA-seq transcripts data, it leads to problems with the accuracy of mitochondrial annotations and the inability to understand RNA processing. In this study, we assembled and annotated the mitogenome of eight Beauveria strains using Illumina DNA and RNA sequencing data. The circular mitogenome of eight Beauveria strains ranged from 26,850 bp (B. caledonica strain ATCC 64970) to 35,999 bp (B. brongniartii strain GYU-BMZ03), with the intronic insertions accounting for most of the size variation, thus contributing to a total mitochondrial genome (mitogenome) size of 7.01% and 28.95%, respectively. Intron number variations were not directly related to the evolutionary relationship distance. Besides ribosomal protein S3 (rps3), most introns are lost too quickly and lack the stability of protein-coding genes. The short RNA-seq reads from next-generation sequencing can improve the mitochondrial annotation accuracy and help study polycistronic transcripts and RNA processing. The transcription initiation sites may be located in the control region. Most introns do not serve as taxonomic markers and also lack open reading frames (ORFs). We assumed that the poly A tail was added to the polycistronic transcript before splicing and one polycistronic transcript (trnM (1)-trnL (1)-trnA-trnF-trnK-trnL (2)-trnQ-trnH-trnM (2)-nad2-nad3-atp9-cox2-trnR (1)-nad4L-nad5-cob-trnC-cox1-trnR (2)-nad1-nad4-atp8-atp6-rns-trnY-trnD-trnS-trnN-cox3-trnG-nad6-trnV-trnI-trnS-trnW-trnP-rnl(rps3)-trnT-trnE-trnM (3)) was first processed from the mitogenome and was subsequently processed into smaller mono-, di-, or tricistronic RNAs.

Complete mitochondrial genome of Pseudoglomeris magnifica (Shelford, 1907) (Insecta: Dictyoptera: Blaberidae).

Pseudoglomeris magnifica (Shelford, 1907) is bred as a pet because of its beautiful appearance. Its complete mitochondrial genome (GenBank accession number MW630139), obtained from the Manwan Town population, was characterized as the first complete mitogenome of the genus Pseudoglomeris. The mitogenome consists of a circular DNA molecule of 16,627 bp with 76.23% AT content. It comprises 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region. The PCGs have the traditional ATN (Met) start codon, except cox1 and nad1 (which have TTG (Met) as the start codon), and are terminated by the traditional TAN stop codon.

Heat wave event facilitates defensive responses in invasive C3 plant Ambrosia artemisiifolia L. under elevated CO2 concentration to the detriment of Ophraella communa.

To predict and mitigate the effects of climate change on communities and ecosystems, the joint effects of extreme climatic events on species interactions need to be understood. Using the common ragweed (Ambrosia artemisiifolia L.)-leaf beetle (Ophraella communa) system, we investigated the effects of heat wave and elevated CO2 on common ragweed growth, secondary metabolism, and the consequent impacts on the beetle. The results showed that elevated CO2 and heat wave facilitated A. artemisiifolia growth; further, A. artemisiifolia accumulated large amounts of defensive secondary metabolites. Being fed on A. artemisiifolia grown under elevated CO2 and heat wave conditions resulted in the poor performance of O. communa (high mortality, long development period, and low reproduction). Overall, under elevated CO2, heat wave improved the defensive ability of A. artemisiifolia against herbivores. On the other hand, enhanced adaptability to climatic changes may aggravate invasive plant distribution, posing a challenge to the control of invasive plants in the future.

Complete mitochondrial genome of Morphostenophanes yunnanus (Zhou, 2020) (Insecta: Coleoptera: Tenebrionidae) and phylogenetic analysis.

Morphostenophanes yunnanus (Zhou, 2020) is widely distributed from central to eastern Yunnan with distinct geographical variations in morphology. Beetles were collected in Manwan Town, and a mitochondrial genome sequence (GenBank accession number MZ298928) of this species was sequenced using the MGI-SEQ 2000 platform, assembled using NOVOPlasty v4.3.1, and characterized. The mitogenome was a circular DNA molecule of 15,690 bp with 64.710% AT content, which comprised 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The protein-coding genes showed the typical ATN (Met) and TTG (Met) start codons, except nad1 and cox1 (TTG as start codon), and were terminated by typical TAN stop codons. The maximum-likelihood polygenetic tree was generated using protein sequences of thirteen protein-coding regions of seventeen mitogenomes with mtREV + G + F + I with 1000 replicates under the Bayesian information criterion using MEGA 11, which showed that M. yunnanus was the most closely related to M. sinicus. This study provides essential genetic and molecular data for phylogenetic analyses of the genus Morphostenophanes.

Single-cell analysis of COVID-19, sepsis, and HIV infection reveals hyperinflammatory and immunosuppressive signatures in monocytes.

The mortality risk of coronavirus disease 2019 (COVID-19) patients has been linked to the cytokine storm caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding the inflammatory responses shared between COVID-19 and other infectious diseases that feature cytokine storms may therefore help in developing improved therapeutic strategies. Here, we use integrative analysis of single-cell transcriptomes to characterize the inflammatory signatures of peripheral blood mononuclear cells from patients with COVID-19, sepsis, and HIV infection. We identify ten hyperinflammatory cell subtypes in which monocytes are the main contributors to the transcriptional differences in these infections. Monocytes from COVID-19 patients share hyperinflammatory signatures with HIV infection and immunosuppressive signatures with sepsis. Finally, we construct a "three-stage" model of heterogeneity among COVID-19 patients, related to the hyperinflammatory and immunosuppressive signatures in monocytes. Our study thus reveals cellular and molecular insights about inflammatory responses to SARS-CoV-2 infection and provides therapeutic guidance to improve treatments for subsets of COVID-19 patients.

Complete mitochondrial genome of Morphostenophanes sinicus (Zhou, 2020) (Insecta: Coleoptera: Tenebrionidae).

The genus Morphostenophanes is a small arboreal group of darkling beetles that are endemic to the Oriental region. The complete mitochondrial genome of the M. sinicus population from the Manwan Town was first characterized. The mitogenome consisted of a circular DNA molecule of 15,662 bp with a 66.352% AT content. It comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. The PCGs have a typical ATN (Met) start codon, except for nad1 (TTG as a start codon), and are terminated by typical TAN stop codons.

The complete mitochondrial genome of Pachytriton granulosus (Chang, 1933) (Amphibia: Caudata: Salamandridae).

Complete mitochondrial genome (GenBank accession number MN073499) for Pachytriton granulosus (Amphibia: Caudata: Salamandridae) was obtained with Sanger sequencing and assembled manually. The mitogenome consists of a circular DNA molecule of 16,288 bp, with 68.51% AT content. It comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The protein-coding genes have typical ATN (Met) start codons, except cox1 (GTG as start codon), and are terminated by typical TAN stop codons, except nad6 (AGA as start codon).

Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm.

Several studies show that the immunosuppressive drugs targeting the interleukin-6 (IL-6) receptor, including tocilizumab, ameliorate lethal inflammatory responses in COVID-19 patients infected with SARS-CoV-2. Here, by employing single-cell analysis of the immune cell composition of two severe-stage COVID-19 patients prior to and following tocilizumab-induced remission, we identify a monocyte subpopulation that contributes to the inflammatory cytokine storms. Furthermore, although tocilizumab treatment attenuates the inflammation, immune cells, including plasma B cells and CD8+ T cells, still exhibit robust humoral and cellular antiviral immune responses. Thus, in addition to providing a high-dimensional dataset on the immune cell distribution at multiple stages of the COVID-19, our work also provides insights into the therapeutic effects of tocilizumab, and identifies potential target cell populations for treating COVID-19-related cytokine storms.