Identifying a potentially invasive population in the native range of a species: The enlightenment from the phylogeography of the yellow spotted stink bug, Erthesina fullo (Hemiptera: Pentatomidae)

The yellow spotted stink bug (YSSB), Erthesina fullo (Thunberg, 1783) is an important Asian pest that has recently successfully invaded Europe and an excellent material for research on the initial stage of biological invasion. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of YSSB for the first time based on population genetic methods [using double digest restriction-site associated DNA (ddRAD) data and mitochondrial COI and CYTB] and ecological niche modelling. The results showed that four lineages (east, west, southwest, and Hainan Island) were established in the native range with a strong east-west differentiation phylogeographical structure, and the violent climate fluctuation might cause population divergence during the Middle and Upper Pleistocene. In addition, land bridges and monsoon promote dispersal and directional genetic exchanging between island populations and neighboring continental populations. The east lineage (EA) was identified as the source of invasion in Albania. EA had the widest geographical distribution among all other lineages, with a star-like haplotype network with the main haplotype as the core. It also had a rapid population expansion history, indicating that the source lineage might have stronger diffusion ability and adaptability. Our findings provided a significant biological basis for fine tracking of invasive source at the lineage or population level and promote early invasion warning of potential invasive species on a much subtler lineage level.

Shared phylogeographic patterns and environmental responses of co-distributed soybean pests: Insights from comparative phylogeographic studies of Riptortus pedestris and Riptortus linearis in the subtropics of East Asia

Comparative phylogeographic studies of closely related species sharing co-distribution areas can elucidate the role of shared historical factors and environmental changes in shaping their phylogeographic pattern. The bean bugs, Riptortus pedestris and Riptortus linearis, which both inhabit subtropical regions in East Asia, are recognized as highly destructive soybean pests. Many previous studies have investigated the biological characteristics, pheromones, chemicals and control mechanisms of these two pests, but few studies have explored their phylogeographic patterns and underlying factors. In this study, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) dataset to investigate phylogeographic patterns and construct ecological niche models (ENM) for both Riptortus species. Our findings revealed similar niche occupancies and population genetic structures between the two species, with each comprising two phylogeographic lineages (i.e., the mainland China and the Indochina Peninsula clades) that diverged approximately 0.1 and 0.3 million years ago, respectively. This divergence likely resulted from the combined effects of temperatures variation and geographical barriers in the mountainous regions of Southwest China. Further demographic history and ENM analyses suggested that both pests underwent rapid expansion prior to the Last Glacial Maximum (LGM). Furthermore, ENM predicts a northward shift of both pests into new soybean-producing regions due to global warming. Our study indicated that co-distribution soybean pests with overlapping ecological niches and similar life histories in subtropical regions of East Asia exhibit congruent phylogeographic and demographic patterns in response to shared historical biogeographic drivers.

Phylogenetic placement and comparative analysis of the mitochondrial genomes of Idiostoloidea (Hemiptera: Heteroptera)

The classification system and the higher level phylogenetic relationships of Pentatomomorpha, the second largest infraorder of Heteroptera (Insecta: Hemiptera), have been debated and remain controversial over decades. In particular, the placement and phylogenetic relationship of Idiostoloidea are not well resolved, which hampers a better understanding of the evolutionary history of Pentatomomorpha. In this study, for the first time, we reported the complete mitochondrial genome for two narrowly distributed families of Idiostoloidea (including Idiostolidae and Henicocoridae), respectively. The length of the mitochondrial genome of Monteithocoris hirsutus and Henicocoris sp. is 16,632 and 16,013 bp, respectively. The content of AT is ranging from 75.15% to 80.48%. The mitogenomic structure of Idiostoloidea is highly conservative and there are no gene arrangements. By using the Bayesian inference, maximum likelihood, and Bayesian site-heterogeneous mixture model, we inferred the phylogenetic relationships within Pentatomomorpha and estimated their divergence times based on concatenated mitogenomes and nuclear ribosomal genes. Our results support the classification system of six superfamilies within Pentatomomorpha and confirm the monophyletic groups of each superfamily, with the following phylogenetic relationships: (Aradoidea + (Pentatomoidea + (Idiostoloidea + (Coreoidea + (Pyrrhocoroidea + Lygaeoidea))))). Furthermore, estimated divergence times revealed that most pentatomomorphan superfamilies and families diverged during the Late Jurassic to Early Cretaceous, which coincides with the explosive radiation of angiosperms.

Identification and expression patterns of somatic piRNAs and PIWI genes in Riptortus pedestris (Hemiptera: Alydidae)

RNA interference (RNAi)-based gene silencing is a feasible and sustainable technology for the management of hemipteran pests by double-stranded RNA involvement, including small-interfering RNA, microRNA, and Piwi-interacting RNA (piRNA) pathways, that may help to decrease the usage of chemical insecticides. However, only a few data are available on the somatic piRNAs and their biogenesis genes in Riptortus pedestris, which serves as a significant pest of soybean (Glycine max). In this study, two family members of the PIWI gene were identified and characterized in R. pedestris, containing Argonaute3 (RpAgo3) and Aubergine (RpAub) genes with conserved protein domains, and their clusters were validated by phylogenetic analysis. In addition, they were widely expressed in all developmental stages of the whole body of R. pedestris and had lower expression levels in R. pedestris guts under different rearing conditions based on previous transcriptome sequencing. Furthermore, abundant clean reads were filtered to a total number of 45,998 piRNAs with uridine bias at the first nucleotide (nt) position and 26-32 nt in length by mapping onto the reference genome of R. pedestris according to our previous whole-transcriptome sequencing. Finally, our data revealed that gut bacterial changes were significantly positively or negatively associated with differentially expressed piRNAs among the five comparison groups with Pearson correlation analysis. In conclusion, these findings paved new avenues for the application of RNAi-based biopesticides for broad-spectrum hemipteran pest control.

Mitogenomes Provide Insights into the Species Boundaries and Phylogenetic Relationships among Three Dolycoris Sloe Bugs (Hemiptera: Pentatomidae) from China

(1) Background: The three sloe bugs, Dolycoris baccarum, Dolycoris indicus, and Dolycoris penicillatus, are found in the Chinese mainland and are morphologically similar. The species boundaries and phylogenetic relationships of the three species remain uncertain; (2) Methods: In this study, we generated multiple mitochondrial genomes (mitogenomes) for each of the three species and conducted comparative mitogenomic analysis, species delimitation, and phylogenetic analysis based on these data; (3) Results: Mitogenomes of the three Dolycoris species are conserved in nucleotide composition, gene arrangement, and codon usage. All protein-coding genes (PCGs) were found to be under purifying selection, and the ND4 evolved at the fastest rate. Most species delimitation analyses based on the COI gene and the concatenated 13 PCGs retrieved three operational taxonomic units (OTUs), which corresponded well with the three Dolycoris species identified based on morphological characters. A clear-cut barcode gap was discovered between the interspecific and intraspecific genetic distances of the three Dolycoris species. Phylogenetic analyses strongly supported the monophyly of Dolycoris, with interspecific relationship inferred as (D. indicus + (D. baccarum + D. penicillatus)); (4) Conclusions: Our study provides the first insight into the species boundaries and phylogenetic relationships of the three Dolycoris species distributed across the Chinese mainland.

Limits of mitochondrial genes in delimiting species within a Carbula species complex (Hemiptera: Pentatomidae)

Molecular data has become a powerful tool for species delimitation, particularly among those that present limited morphological differences; while the mitochondrial genome, with its moderate length, low cost of sequencing and fast lineage sorting, has emerged as a practical data set. Due to the limited morphological differences among the closely related species of Carbula Stål 1865, the species boundaries between Carbula abbreviata (Motschulsky, 1866), Carbula humerigera (Uhler, 1860), and Carbula putoni (Jakovlev, 1876) have remained particularly unclear. In this study, we applied two phylogenetic reconstruction methods to two data sets (mitogenome and COI) to assess the phylogeny of Carbula distributed in Asia, and five species delimitation methods to determine the boundaries between East Asian Carbula species. Our phylogenetic analyses showed Carbula to be paraphyletic; the seven known species distributed within East Asia to form a single monophyletic group, and within this, C. abbreviata, C. humerigera, C. putoni and middle-type to comprise a C. humerigera species complex. Our results show that mitogenome data alone, while effective in the differentiation of more distantly related Carbula species, is not sufficient to accurately delimit the species within this newly described complex.

Changes in the gut bacterial community affect miRNA profiles in Riptortus pedestris under different rearing conditions

Insects possess complex and dynamic gut microbial system, which contributes to host nutrient absorption, reproduction, energy metabolism, and protection against stress. However, there are limited data on interactions of host-gut bacterial microbiota through miRNA (microRNA) regulation in a significant pest, Riptortus pedestris. Here, we performed the 16S rRNA amplicon sequencing and small RNA sequencing from the R. pedestris gut under three environmental conditions and antibiotic treatment, suggesting that we obtained a large amount of reads by assembly, filtration and quality control. The 16S rRNA amplicon sequencing results showed that the abundance and diversity of gut bacterial microbiota were significantly changed between antibiotic treatment and other groups, and they are involved in metabolism and biosynthesis-related function based on functional prediction. Furthermore, we identified different numbers of differentially expressed unigenes (DEGs) and differentially expressed miRNAs (DEMs) based on high-quality mappable reads, which were enriched in various immune-related pathways, including Toll-like receptor, RIG-I-like receptor, NOD-like receptor, JAK/STAT, PI3K/Akt, NF-κB, MAPK signaling pathways, and so forth, using GO and KEGG enrichment analysis. Later on, the identified miRNAs and their target genes in the R. pedestris gut were predicted and randomly selected to construct an interaction network. Finally, our study indicated that alterations in the gut bacterial microbiota are significantly positively or negatively associated with DEMs of the Toll/Imd signaling pathway with Pearson correlation analysis. Taken together, the results of our study lay the foundation for further deeply understanding the interactions between the gut microbiota and immune responses in R. pedestris through miRNA regulation, and provide the new basis for pest management in hemipteran pests.

Integrated analysis of miRNA profiles and gut bacterial changes in Altica viridicyanea following antibiotic treatment

The gut bacteria involves in insect homeostasis by playing essential roles in host physiology, metabolism, innate immunity, and so forth. microRNAs (miRNAs) are endogenous small noncoding RNAs that posttranscriptionally regulate gene expression to affect immune or metabolic processes in insects. For several non-model insects, the available knowledge on the relationship between changes in the gut bacteria and miRNA profiles is limited. In this study, we investigated the gut bacterial diversity, composition, and function from Altica viridicyanea feeding on normal- and antibiotic-treated host plants using 16S rRNA amplicon sequencing; antibiotics have been shown to affect the body weight and development time in A. viridicyanea, suggesting that the gut bacteria of the normal sample were more diverse and abundant than those of the antibiotic-fed group, and most of them were involved in various physical functions by enrichment analysis. Furthermore, we executed small RNA transcriptome sequencing using the two experimental groups to obtain numerous sRNAs, such as piRNAs, siRNAs, and known and novel miRNAs, by data mapping and quality control, and furthermore, a total of 224 miRNAs were identified as significantly differentially expressed miRNAs, of which some DEMs and their target genes participated in immune- and metabolism-related pathways based on GO and KEGG annotation. Besides, regarding the regulatory roles of miRNA and target genes, a interaction network of DEM-target gene pairs from eight immune- or metabolism-related signaling pathways were constructed. Finally, we discovered that DEMs from above pathways were significantly positively or negatively correlated with gut bacterial alterations following antibiotic treatment. Collectively, the observations of this study expand our understanding of how the disturbance of gut bacteria affects miRNA profiles in A. viridicyanea and provide new valuable resources from extreme ranges for future studies on the adaptive evolution in insects.

The lncRNA-mediated ceRNA network of Altica viridicyanea is involved in the regulation of the Toll/Imd signaling pathway under antibiotic treatment

Long noncoding RNAs (lncRNAs) play significant roles in the regulation of mRNA expression or in shaping the competing endogenous RNA (ceRNA) network by targeting miRNA. The insect gut is one of the most important tissues due to direct contact with external pathogens and functions in the immune defense against pathogen infection through the innate immune system and symbionts, but there are limited observations on the role of the lncRNA-involved ceRNA network of the Toll/Imd pathway and correlation analysis between this network and bacterial microbiota in the Altica viridicyanea gut. In this research, we constructed and sequenced six RNA sequencing libraries using normal and antibiotic-reared samples, generating a total of 17,193 lncRNAs and 26,361 mRNAs from massive clean data by quality control and bioinformatic analysis. Furthermore, a set of 8,539 differentially expressed lncRNAs (DELs) and 13,263 differentially expressed mRNAs (DEMs), of which related to various immune signaling pathways, such as the Toll/Imd, JAK/STAT, NF-κB, and PI3K-Akt signaling pathways, were obtained between the two experimental groups in A. viridicyanea. In addition, numerous GO and KEGG enrichment analyses were used to annotate the DELs and their target genes. Moreover, six Toll family members and nineteen signal genes from the Toll/Imd signaling pathway were identified and characterized using online tools, and phylogenetic analyses of the above genes proved their classification. Next, a lncRNA-miRNA-mRNA network of the Toll/Imd pathway was built, and it contained different numbers of DEMs in this pathway and related DELs based on prediction and annotation. In addition, qRT-PCR validation and sequencing data were conducted to show the expression patterns of the above DELs and DEMs related to the Toll/Imd signaling pathway. Finally, the correlated investigations between DELs or DEMs of the Toll/Imd signaling pathway and most changes in the gut bacterial microbiota revealed significantly positive or negative relationships between them. The present findings provide essential evidence for innate immune ceRNAs in the beetle gut and uncover new potential relationships between innate immune pathways and the gut bacterial microbiota in insects.

Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae)

Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.

Mechanical characteristics analysis and control algorithm for floating raft system with mass variation

The ship floating raft system adopts the integrated design of large liquid tanks and rafts, which can optimize the arrangement in the cabin and increase the intermediate mass of the system to achieve efficient vibration isolation of equipment. One of the major challenges is that the change of liquid mass in the tank will cause displacement of the raft, which will change the modal characteristics of the system and affect the stability of the vibration isolation system performance. This paper establishes a mechanical analysis model of a floating raft system under time-varying liquid mass conditions. Taking a ship variable mass floating raft system as the research object, the effect of mass change on the characteristics of raft displacement, isolator load distribution, and modal frequency of the vibration isolation system is analyzed. The analysis shows that when the liquid tank goes from full load to no-load state, its mass change accounts for 40% of the total mass of the raft, which will cause a large displacement of the raft and change the low order modal frequency of the system, bringing the risk of equipment safety and vibration isolation performance degradation. Therefore, an adaptive variable load control method is proposed to realize the raft attitude balance and load equalization optimization under the variable mass condition of the floating raft air spring system. The test results show that the proposed control method can automatically adapt to the large mass gradual change from full load to no load of the liquid tank on the raft, and control the displacement of the raft structure from about 10 mm to 1.5 mm, which effectively ensures the stability of the air spring system performance.

Out of East Asia: Early Warning of the Possible Invasion of the Important Bean Pest Stalk-Eyed Seed Bug Chauliops fallax (Heteroptera: Malcidae: Chauliopinae)

The short stay at the beginning of the invasion process is a critical time for invasive species identification and preventing invasive species from developing a wider distribution and significant economic impact. The stalk-eyed seed bug Chauliops fallax is an important agricultural pest of soybean and was first reported to occur outside East Asia. Here, we reported the native evolutionary history, recent invasion history, and potential invasion threats of C. fallax for the first time based on population genetic methods and ecological niche modelling. The results showed that four native East Asian genetic groups (EA, WE, TL, and XZ) were well supported, showing an east-west differentiation pattern consistent with the geographical characteristics of three-step landforms in China. Two main haplotypes existed: Hap1 might have experienced a rapid northwards expansion process after the LGM period, and Hap5 reflected local adaptation to the environment in southeastern China. The Kashmir sample was found to come from the recent invasion of populations in the coastal areas of southern China. Ecological niche modelling results suggested that North America has a high risk of invasion, which might pose a serious threat to local soybean production. In addition, with future global warming, the suitable habitat in Asia will move towards the higher latitude region and gradually deviate from the soybean planting area, which indicates the threat of C. fallax to soybean production in Asia will decrease in the future. The results could provide new insights into the monitoring and management of this agricultural pest in the early invasion stage.

Climate change impacts on the potential worldwide distribution of the soybean pest, Piezodorus guildinii (Hemiptera: Pentatomidae)

The redbanded stink bug, Piezodorus guildinii (Westwood, 1837), is a highly destructive soybean pest native to the Neotropical Region. In the past 60 yr, P. guildinii has been observed to expand its distribution in North and South America, causing significant soybean yield losses. In order to predict the future distribution direction of P. guildinii and create an effective pest control strategy, we projected the potential global distribution of P. guildinii using 2 different emission scenarios, Shared Socioeconomic Pathways 126 and 585, and 3 Earth system models, with the maximum entropy niche model (MaxEnt). Then, the predicted distribution areas of P. guildinii were jointly analyzed with the main soybean-producing areas to assess the impact for different soybean region. Our results showed that temperature is the main environmental factor limiting the distribution of P. guildinii. Under present climate conditions, all continents except Antarctica have suitable habitat for P. guildinii. These suitable habitats overlap with approximately 45.11% of the total global cultivated soybean areas. Moreover, P. guildinii was predicted to expand its range in the future, particularly into higher latitudes in the Northern hemisphere. Countries, in particular the United States, where soybean is widely available, would face a management challenge under global warming. In addition, China and India are also high-risk countries that may be invaded and should take strict quarantine measures. The maps of projected distribution produced in this study may prove useful in the future management of P. guildinii and the containment of its disruptive effects.

Chromosome-level genome of the bean bug Megacopta cribraria in native range, provides insights into adaptation and pest management

Megacopta cribraria, a bean pest causing tremendous economic losses in Asia, was discovered in North America in 2009. Although M. cribraria has become the focus of research on biological invasion and pest management, the lack of genomic resources limits in-depth studies. Here, we report the first chromosome-level genome of M. cribraria using Illumina, PacBio, and Hi-C data. The assembled genome size was 699.65 Mb, with a contig N50 of 1.43 Mb and a scaffold N50 of 109.27 Mb. >97.51 % of bases were successfully anchored to six chromosomes. Through genome annotation, a total of 13,308 coding genes were predicted, 96.3 % of which were successfully accessed function. Expanded gene families were involved in proteolysis, protein metabolism and nitrogen metabolism reflected the underlying genome basis for host adaptation during evolution. Transcriptome analysis revealed different gene expression patterns in antenna, mouthpart, head, leg, wing, and carcass body of the adult M. cribraria, respectively. Moreover, the expression profiles of the odorant receptor genes indicated the potential target genes for pest control. The high-quality chromosome-level genome will benefit further research on the adaptation, evolution, and population genetics of the M. cribraria that will assist in the pest management and tracking the biological invasion routes.

Taxonomic review of Manocoreini with description of a new species from China (Hemiptera, Heteroptera, Coreidae)

In the present paper, all seven species of Manocoreini are reviewed, and a new species Manocoreus hsiaoisp. nov. is described from Guangxi, China. Photographs of habitus of all species, and detailed structures of the new species and type species of Manocoreus Hsiao, 1964 are provided. All species of Manocoreini of the world are keyed. A distribution map of all species is also provided.

Phylogeny and historical biogeography of the water boatmen (Insecta: Hemiptera: Heteroptera: Nepomorpha: Corixoidea)

The water boatmen of Corixoidea, a group of aquatic bugs with more than 600 extant species, is one of the largest superfamilies of Nepomorpha. Contrary to the other nepomorphan lineages, the Corixoidea are most diverse in the Laurasian remnant Holarctic region. To explicitly test whether the present-day Holarctic distribution of diverse corixids is associated with the arising of the Laurasian landmass that was separated from Gondwana, we investigated the phylogeny, divergence times and historical biogeography of Corixoidea based on morphological and molecular characters sampled from 122 taxa representing all families, subfamilies, tribes and approximately 54 % of the genera. Our results were largely congruent with the phylogenetic relationships within the established nepomorphan phylogenetic context. The fossil calibrated chronogram, diversification analysis and ancestral ranges reconstruction indicated that Corixoidea began to diversify in Gondwana in the late Triassic approximately at 224 Ma and the arising of the most diverse subfamily Corixinae in Corixidae in the Holarctic region was largely congruent with the time of separation of Laurasia from Gondwana. The large-scale expansion of the temperate and cold zones on the northward-moving Laurasian landmass after the breakup of the Pangea provided new aquatic niches and ecological opportunities for promoting rapid diversification for the Holarctic corixid lineage.

The first discovery of Tc1 transposons in yeast

Background

Identification of transposons without close homologs is still a difficult task. IS630/Tc1/mariner transposons, classified into a superfamily, are probably the most widespread DNA transposons in nature. Tc1/mariner transposons have been discovered in animals, plants, and filamentous fungi, however, not in yeast.

Results

In the present study, we report the discovery of two intact Tc1 transposons in yeast and filamentous fungi, respectively. The first one, named Tc1-OP1 (DD40E), represents Tc1 transposons in Ogataea parapolymorpha. The second one, named Tc1-MP1 (DD34E), represents Tc1 transposons in the Rhizopodaceae and Mucoraceae families. As a homolog of Tc1-OP1 and Tc1-MP1, IS630-AB1 (DD34E) was discovered as an IS630 transposon in Acinetobacter spp.

Conclusion

Tc1-OP1 is not only the first reported Tc1 transposon in yeast, but also the first reported nonclassical Tc1 transposon. Tc1-OP1 is the largest of IS630/Tc1/mariner transposons reported to date and significantly different from others. Notably, Tc1-OP1 encodes a serine-rich domain and a transposase, extending the current knowledge of Tc1 transposons. The phylogenetic relationships of Tc1-OP1, Tc1-MP1 and IS630-AB1 indicated that these transposons had evolved from a common ancestor. Tc1-OP1, Tc1-MP1 and IS630-AB1 can be used as reference sequences to facilitate the identification of IS630/Tc1/mariner transposons. More Tc1/mariner transposons will be identified in yeast, following our discovery.

The anthropogenic effect of land use on population genetics of Malcus inconspicuus

Since the beginning of the Holocene era, human activities have seriously impacted animal habitats and vegetative environments. Species that are dependent on natural habitats or with narrow niches might be more severely affected by habitat changes. Malcus inconspicuus is distributed in subtropical China and highly dependent on the mountain environment. Our study investigated the role of the mountainous landscape in the historical evolution of M. inconspicuus and the impact of Holocene human activities on it. A phylogeographical approach was implemented with integrative datasets including double-digest restriction site-associated DNA (ddRAD), mitochondrial data, and distribution data. Three obvious clades and an east-west phylogeographical pattern were found in subtropical China. Mountainous landscape has "multifaceted" effects on the evolutionary history of M. inconspicuus, it has contributed to population differentiation, provided glacial refuges, and provided population expansion corridors during the postglacial period. The effective population size (Ne) of M. inconspicuus showed a sharp decline during the Holocene era, which revealed a significantly negative correlation with the development of cropland in a hilly area at the same time and space. It supported that the species which are highly dependent on natural habitats might undergo greater impact when the habitat was damaged by agricultural activities and we should pay more attention to them, especially in the land development of their distribution areas.

Species boundary and phylogeographical pattern provide new insights into the management efforts of Megacopta cribraria (Hemiptera: Plataspidae), a bean bug invading North America

BACKGROUND

Correct identification together with information on distribution range, geographical origin and evolutionary history are the necessary basis for the management and control of invasive species. The bean bug Megacopta cribraria is a crucial agricultural pest of soybean. Recently, M. cribraria has invaded the United States and spread rapidly, causing severe reductions in soybean yields. However, the species boundary and phylogeographical pattern of this invasive bean bug are still unclear.

RESULTS

The results of different species delimitation methods (Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Bayesian Poisson Tree Processes and Bayesian Phylogenetics and Phylogeography) strongly demonstrated that M. cribraria and Megacopta punctatissima represent the same species. M. punctatissima should not be considered a distinct species but rather a variety of M. cribraria. Phylogenetic analyses revealed three well-supported clades (Southeast Asia [SEA], East Asia continent [EAC] and Japan [JA]) with distinct geographical structures in the M. cribraria-M. punctatissima complex. The SEA clade was at the base of the phylogenetic tree, and the sister relationship between the EAC clade and JA clade was strongly supported. The split between the EAC clade and JA clade occurred at approximately 0.71 Ma, corresponding to the submergence period of the East China Sea land bridge.

CONCLUSION

This study clarified the species boundary between M. cribraria and its closely related species and revealed the phylogeographical pattern and evolutionary history of M. cribraria. The species delimitation and phylogeography results achieved in this study could provide new insights into the monitoring and management of this agricultural pest. © 2022 Society of Chemical Industry.

Two new stick insect species of Sosibia Stål (Phasmatodea: Lonchodidae: Necrosciinae) from China and the first report on mitochondrial genomes of this genus

We describe and illustrate two new species of Sosibia from China: Sosibia gibba sp. nov. and Sosibia ovata sp. nov. This report includes a key to Sosibia species from China and a description of the distribution area in China. The two mitochondrial genomes of these new Sosibia species were sequenced and annotated for the first time. The compositional biases, codon usage, nucleotide composition, and construct tRNA secondary structures of the two mitogenomes were analyzed. The phylogenetic relationships based on the mitogenomes using Bayesian inference and maximum likelihood methods supported the monophyly of Necrosciinae and divided it into two distinct clades: A: (Sipyloidea + [Sosibia + Calvisia]); and B: (Neohirasea + Micadina).

Precise annotation of Drosophila mitochondrial genomes leads to insights into AT-rich regions

In the present study, we performed precise annotation of Drosophila melanogaster, D. simulans, D. grimshawi, Bactrocera oleae mitochondrial (mt) genomes using pan RNA-seq analysis. Using PacBio cDNA-seq data from D. simulans, we precisely annotated the Transcription Initiation Sites (TISs) of the mt Heavy and Light strands in Drosophila mt genomes and reported that the polyA(+) and polyA(-) motifs in the CRs are associated with TISs. The discovery of the conserved polyA(+) and polyA(-) motifs provides insights into many polyA and polyT sequences in CRs of insect mt genomes, leading to reveal the mt transcription and its regulation in invertebrates. Notably, we propose that: (1) polyA/polyT motifs in CRs function as signals to initiate mtDNA transcription; (2) the duplication, recombination or mutation of these polyA/polyT sequences formed the AT-rich regions during evolution; and (3) since CRs of many invertebrate species still contain many polyA/polyT sequences, there is a high probability that several TISs and TTSs exist in invertebrate mt genomes.

Climate Warming Since the Holocene Accelerates West-East Communication for the Eurasian Temperate Water Strider Species Aquarius paludum

Holocene climate warming has dramatically altered biological diversity and distributions. Recent human-induced emissions of greenhouse gases will exacerbate global warming and thus induce threats to cold-adapted taxa. However, the impacts of this major climate change on transcontinental temperate species are still poorly understood. Here, we generated extensive genomic datasets for a water strider, Aquarius paludum, which was sampled across its entire distribution in Eurasia and used these datasets in combination with ecological niche modeling (ENM) to elucidate the influence of the Holocene and future climate warming on its population structure and demographic history. We found that A. paludum consisted of two phylogeographic lineages that diverged in the middle Pleistocene, which resulted in a “west–east component” genetic pattern that was probably triggered by Central Asia-Mongoxin aridification and Pleistocene glaciations. The diverged western and eastern lineages had a second contact in the Holocene, which shaped a temporary hybrid zone located at the boundary of the arid–semiarid regions of China. Future predictions detected a potentially novel northern corridor to connect the western and eastern populations, indicating west–east gene flow would possibly continue to intensify under future warming climate conditions. Further integrating phylogeographic and ENM analyses of multiple Eurasian temperate taxa based on published studies reinforced our findings on the “west–east component” genetic pattern and the predicted future northern corridor for A. paludum. Our study provided a detailed paradigm from a phylogeographic perspective of how transcontinental temperate species differ from cold-adapted taxa in their response to climate warming.

Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae

Coreoidea (Insecta: Hemiptera: Heteroptera) is a widely distributed and agriculturally important bugs. However, the phylogeny of Coreoidea lacked consensus on higher-level relationships and several studies by comparative morphological characters and molecular data suggested the non-monophyly of two families: Coreidae and Alydidae. The mitochondrial genome (mitogenome) has long been thought to be a significant marker to understand phylogenetic relationships, but the mitogenome in Alydidae is scarce to date. In the present study, we gathered the mitogenomes of 28 species from four families of Coreoidea excluding Hyocephalidae (Alydidae, Coreidae, Rhopalidae, and Stenocephalidae), including four newly sequenced mitogenomes of Alydidae, and conducted mitogenomic organization and phylogenetic studies. We used maximum likelihood and Bayesian inference methods to infer the higher-level phylogeny from the perspective of mitogenomes, primarily to investigate the phylogenetic relationship betweeen Coreidae and Alydidae. We add evidence that neither Alydidae nor Coreidae are monophyletic based on mitogenomes. Newly sequenced mitogenomes of Alydidae have traditional gene structure and gene rearrangement was not found. Alydinae was always recovered as closely related to Pseudophloeinae of the coreid subfamily with high support. The placement of the coreid subfamily Hydarinae and alydid subfamily Micrelytrinae are unstable depending on approach used. In terms of the length and nucleotide composition of the protein coding genes in mitogenomes, Pseudophloeinae and Hydarinae of coreid were more similar to Alydidae. The unsettled classification issues of Coreidae and Alydidae by mitogenomes were demonstrated in this work, indicating that further study is needed.

Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions

Background

Currently, methylotrophic yeasts (e.g., Pichia pastoris, Ogataea polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains-CBS4732, NCYC495, and DL-1. However, the relationship between CBS4732, NCYC495, and DL-1 remains unclear, as the genomic differences between them have not be exactly determined without their high-quality complete genomes. As a nutritionally deficient mutant derived from CBS4732, the O. polymorpha strain CBS4732 ura3Δ (named HU-11) is being used for high-yield production of several important proteins or peptides. HU-11 has the same reference genome as CBS4732 (noted as HU-11/CBS4732), because the only genomic difference between them is a 5-bp insertion.

Results

In the present study, we have assembled the full-length genome of O. polymorpha HU-11/CBS4732 using high-depth PacBio and Illumina data. Long terminal repeat retrotransposons (LTR-rts), rDNA, 5′ and 3′ telomeric, subtelomeric, low complexity and other repeat regions were exactly determined to improve the genome quality. In brief, the main findings include complete rDNAs, complete LTR-rts, three large duplicated segments in subtelomeric regions and three structural variations between the HU-11/CBS4732 and NCYC495 genomes. These findings are very important for the assembly of full-length genomes of yeast and the correction of assembly errors in the published genomes of Ogataea spp. HU-11/CBS4732 is so phylogenetically close to NCYC495 that the syntenic regions cover nearly 100% of their genomes. Moreover, HU-11/CBS4732 and NCYC495 share a nucleotide identity of 99.5% through their whole genomes. CBS4732 and NCYC495 can be regarded as the same strain in basic research and industrial applications.

Conclusion

The present study preliminarily revealed the relationship between CBS4732, NCYC495, and DL-1. Our findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha CBS4732, NCYC495, DL-1, and their derivative strains. The full-length genome of O. polymorpha HU-11/CBS4732 should be included into the NCBI RefSeq database for future studies of Ogataea spp.

The phylogenic position of aschiphasmatidae in euphasmatodea based on mitochondrial genomic evidence

The mitochondrial genome (mitogenome) has been regarded as significant source of data to better understand the phylogenetic relationships within the Euphasmatodea, but no mitogenome in Aschiphasmatoidea has been sequenced to date. In this study, two mitogenomes of Orthomeria smaragdinum and Nanhuaphasma hamicercum of Aschiphasmatidae were sequenced and annotated for the first time. The same mitochondrial gene rearrangement structure was present in the two mitogenomes sequenced, showing as the translocation of tRNA-Arg and tRNA-Asn, which conformed to the tandem duplication-random loss and could be used as a possible synapomorphy for Aschiphasmatidae. The phylogenetic results based on the maximum likelihood (ML) and bayesian inference (BI) methods both showed that Aschiphasmatidae and Neophasmatodea in Euphasmatodea are sister taxa. Although the monophyly of Oriophasmata, Occidophasmata, Diapheromeridae, Phasmatidae, Lonchodidae and Bacilloidea has not been solved, the monophyly of Neophasmatodea and Phyllioidea was well supported.

Transcriptome-wide identification and characterization of toll-like receptors response to Vibrio anguillarum infection in Manila clam (Ruditapes philippinarum)

The Manila clam (Ruditapes philippinarum), one of the major marine aquaculture species in China, is susceptible to infection with the pathogen Vibrio, which results in massive mortality and economic losses. Toll-like receptors (TLRs) are significant pattern recognition receptors (PRRs) of innate immunity that are involved in immune regulation against pathogenic invasion. Molecular characterization of Manila clam TLRs and investigations of their immune functions are essential to prevent and control Vibrio infection. In the present research, eight cDNA sequences of R. philippinarum TLRs (RpTLRs) were identified from previous transcriptome libraries and then classified into four groups, namely, P-TLR (one sequence), V-TLR (one sequence), Ls-TLR (two sequences) and sP-TLR (four sequences), based on the corresponding LRR domain arrangement of their protein structures within the typical TLR motifs. A selective pressure test firstly suggested that the molluscan P-TLR, V-TLR, Ls-TLR and sP-TLR families underwent positive selection, and different numbers of positive selection sites (PSSs) were identified in different domains of the four types of RpTLRs, as determined by PAML and analysis of website data. These findings indicated that the evolution of RpTLRs may be associated with their immune recognition and function. Furthermore, tissue-specific expression analysis showed that all RpTLRs were ubiquitously expressed in all test tissues and were dominant in hemocytes. Quantitative real-time PCR revealed that the cDNA expression of all eight RpTLRs was upregulated after injection with Vibrio anguillarum (P < 0.01) in R. philippinarum hemocytes, revealing that these RpTLRs play important roles in responding to pathogenic stimulation. In summary, these findings provide a foundation for future investigations of the molecular classification and evolutionary patterns of Toll-like receptors in invertebrates, and the innate immune responses of TLR signaling pathways in Mollusca.

Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages

Simple Summary

Riptortus pedestris is a widely distributed pest insect in East Asia that causes considerable economic losses. In this study, we applied the Illumina HiSeq6000 platform to construct and sequence the transcriptome libraries of R. pedestris during all life stages. First, a total of 60,058 unigenes were assembled from raw data, and then annotated and classified with various databases. Furthermore, different numbers of differentially expressed genes were calculated by pairwise comparisons of all life stages, and some of these DEGs were associated with various functions by GO and KEGG analysis. Additionally, a total number of 35,158 SSRs and 715,604 SNPs were identified from all the transcriptome libraries. Finally, we analyzed ten wing formation-related signaling pathways, and detected the molecular and expression characterization of five wing development-related genes by qRT-PCR for all developmental stages of R. pedestris. Collectively, all these data may pave the avenue for exploring the developmental processes of hemimetabolous insects and pest management.

Abstract

Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.

Are population isolations and declines a threat to island endemic water striders? A lesson from demographic and niche modelling of Metrocoris esakii (Hemiptera: Gerridae)

Genetic stochasticity and bottlenecking in the course of Pleistocene glaciations have been identified as threatening the survival of local endemics. However, the mechanisms by which local endemic species balance the influences of these two events remain poorly understood. Here, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) data set, mined mitochondrial sequences and constructed ecological niche models for the island endemic water strider Metrocoris esakii (Hemiptera: Gerridae). We found that M. esakii comprised three divergent lineages (i.e., north, central and south) isolated by geographical barriers and generally experienced population declines with the constriction of suitable areas during the Last Glacial Maximum (LGM). Further demographic model testing and stairway plots revealed a history of recent gene flow among the neighbouring lineages and rapid recovery at the end of the LGM, indicating that M. esakii at least had the potential for an adaptive response to population fragmentation and bottlenecking. The northern lineage did not show genetic bottlenecking during the LGM, which was probably due to its large effective population size (N_e ) from migration, which improved its adaptive potential. Relative to the ddRAD-seq data set, the demographic results based on mitochondrial sequences were less conclusive, showing weak differentiation and oversimplified demographic trajectories for the three genetic lineages. Overall, this study provides some degree of optimism for the survival of island endemic water striders from a demographic perspective, but further evaluation of their extinction risk under the impacts of human activities is required.

Notes on the genus Perittopus Fieber, 1860 (Hemiptera: Heteroptera: Veliidae) with descriptions of three new species from Indochina

Three species of the genus Perittopus Fieber from Indochina are described as new: P. anthracinus sp. n. from Yunnan of China, P. laosensis sp. n. from Laos and P. trizonus sp. n. from Thailand. Photographs of key female and male characters and male genitalic structures are provided, accompanied by a distribution map for the species of Perittopus occurring in Indochina.

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element

Background

In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes. We aimed to: (1) develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal (e.g. Dermacentor silvarum) containing miniscule DNA; (2) provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) detect and analyze mt DNA variation within an individual tick.

Results

These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and can produce deleterious proteins.

Conclusions

We proposed that the accumulation of CNV of STRs in mitochondria may cause aging or diseases. Future tests of the CNV of STRs hypothesis help to ultimately reveal the genetic basis of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.

Molecular and expression characterization of Toll-like receptor family genes from the Anadara sativa (Bivalvia, Arcidae) transcriptome

Innate immunity plays an important role in invertebrates because it provides the first line of protection by recognizing invading microbial pathogens and then activating downstream signaling pathways. However, until now, increasing reports of clam diseases did not include those of Anadara sativa, which are widely distributed and economically important maritime clams. In the present study, transcriptome libraries of untreated (termed H) and Vibrio anguillarum-challenged (termed HV) A. sativa hepatopancreases were constructed and sequenced using the Illumina HiSeq4000 platform. In total, we obtained 78,012,510 and 84,937,516 clean reads from 80,006,030 to 86,871,742 raw data reads, respectively, assembled by different software programs. Furthermore, 150,274 unigenes were generated from 196,003 transcripts, with an N50 length of 1088 bp, and then annotated with the SwissProt, NR, NT, PFAM, KO, GO, KOG and KEGG databases. Moreover, 3982 differentially expressed unigenes (H vs HV) were determined, with 3583 upregulated and 399 downregulated genes. Among these differentially expressed unigenes, 207 unigenes were found using KEGG annotation in 16 immune-related signaling pathways, such as Toll-like receptor (TLR), NOD-like receptor (NLR), and RIG-I-like receptor (RLR) signaling pathways. Finally, we selected 11 full-length TLRs and classified them into 3 groups, namely, one V-TLR, four Ls-TLR and six sP-TLR; furthermore, we validated the increased expression patterns of the 11 TLRs in response to LPS injection. In summary, these results revealed multiple findings on potential immune-related genes, such as the differential expression analysis and annotation based on the A. sativa transcriptome in response to V. anguillarum stimulation, and explored the molecular and expression characterization of A. sativa TLRs, which provide new insights into the innate immune responses and defense mechanisms in shellfish.

A key to species of genus Malcus Stål, with descriptions of four new species from China (Hemiptera: Heteroptera: Malcidae)

Four new species of Malcus Stål are described and illustrated, Malcus alatus sp. nov., Malcus bacillus sp. nov., Malcus externus sp. nov. and Malcus planus sp. nov.. The male of Malcus gibbus Zheng, Zou Hsiao, 1979 is described for the first time. A revised key to species of Malcus of the world is provided.

Morphology lies: a case-in-point with a new non-biting midge species from Oriental China (Diptera, Chironomidae)

Morphological traits are generally indicative of specific taxa, and particularly function as keys in taxonomy and species delimitation. In this study, a non-biting midge species with an Einfeldia-like superior volsella makes it hard to accurately determined based on its morphological characteristics. Molecular genes of two ribosomal genes and three protein-encoding genes were compiled to construct a related genera phylogeny and to address the taxonomic issues. Phylogenetic inference clearly supports the undetermined species as belonging to Kiefferulus. Therefore, a new species classified in the genus Kiefferulus is described and figured as an adult male from Oriental China. The species could be easily distinguished from other species in having an Einfeldia-like superior volsella and a triangular tergite IX.

Phylogeny and diversification of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha)

Climate fluctuations and tectonic reconfigurations associated with environmental changes play large roles in determining patterns of adaptation and diversification, but studies documenting how such drivers have shaped the evolutionary history and diversification dynamics of limnic organisms during the Mesozoic are scarce. Members of the heteropteran infraorder Nepomorpha, or aquatic bugs, are ideal for testing the effects of these determinants on their diversification pulses because most species are confined to aquatic environments during their entire life. The group has a relatively mature taxonomy and is well represented in the fossil record. We investigated the evolution of Nepomorpha based on phylogenetic analyses of morphological and molecular characters sampled from 115 taxa representing all 13 families and approximately 40% of recognized genera. Our results were largely congruent with the phylogenetic relationships inferred from morphology. A divergence dating analysis indicated that Nepomorpha began to diversify in the late Permian (approximately 263 Ma), and diversification analyses suggested that palaeoecological opportunities probably promoted lineage diversification in this group.

Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals

In the present study, we applied our 'precise annotation' to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5' and 3' end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.

The Dose-Response Associations of Sedentary Time with Chronic Diseases and the Risk for All-Cause Mortality Affected by Different Health Status: A Systematic Review and Meta-Analysis

PURPOSE

To determine the dose-response associations of sedentary behaviour with cardiovascular diseases (CVD), cancer, and all-cause mortality, and to examine whether the sedentary-associated all-cause mortality risk was affected by appearance of diabetes and hypertension, physical activity, and body mass index (BMI).

DESIGN

We carried out a systematic review and meta-analysis to search Medline, SportDiscus, and Web of Science for eligible studies.

SETTINGS

Prospective cohort studies that reported sedentary time and CVD, cancer, and mortality incidents.

MEASUREMENTS

Two authors independently extracted data based on predefined criteria. The effect estimates were evaluated by hazard ratios (HRs) with 95% confidences (CIs).

RESULTS

Twenty-four studies met the inclusion criteria. Sitting time showed dose-response associations with CVD, cancer, and all-cause mortality, with each 1-hour increment of sitting time daily accounting for HRs 1.04 (95% CIs 1.02-1.07), 1.01 (1.00-1.02), and 1.03 (1.02-1.03), respectively. The link between sitting time and CVD and all-cause mortality was non-linear (pnon-linear < 0.0001). The relationship between TV viewing and CVD and all-cause mortality was dose-dependent, with HRs 1.07 (1.06-1.09) and 1.04 (1.01-1.06) for per 1-hour increment of TV time every day, respectively. The regression was curved (pnon-linear < 0.0001). When the analysis was stratified by the percentage of diabetes and hypertension, BMI values, and physical activity levels, we found that higher BMI and a greater percentage of diabetes and hypertension further increased all-cause mortality risk in the most sedentary populations, whereas higher physical activity levels decreased it.

CONCLUSION

Sitting time and TV viewing significantly increased cardiovascular, cancer, and mortality risk; the associations were dose-dependent. More importantly, sedentary behaviour in combination with chronic diseases or high BMI increased all-cause mortality risk whereas physical activity was likely to alleviate the adverse associations.

Higher-Order Quantum Ghost Imaging with Ultracold Atoms

Ghost imaging is a quantum optics technique that uses correlations between two beams to reconstruct an image from photons that do not interact with the object being imaged. While pairwise (second-order) correlations are usually used to create the ghost image, higher-order correlations can be utilized to improve the performance. In this Letter, we demonstrate higher-order atomic ghost imaging, using entangled ultracold metastable helium atoms from an s-wave collision halo. We construct higher-order ghost images up to fifth order and show that using higher-order correlations can improve the visibility of the images without impacting the resolution. This is the first demonstration of higher-order ghost imaging with massive particles and the first higher-order ghost imaging protocol of any type using a quantum source.

Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region

In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. The high-resolution annotations cover both entire strands of the mitochondrial genome without any gaps or overlaps. Most of the new annotations were consistent with the previous annotations which had been obtained using PacBio full-length transcripts. Two important findings were that animals transcribe both entire strands of mitochondrial genomes and the tandem repeats in the control region of the E. fullo mitochondrial genome contains the repeated Transcription Initiation Sites (TISs) of the heavy strand. In addition, we found that the copy numbers of tandem repeats showed a great diversity within an individual, suggesting that mitochondrial DNA recombination occurs in an individual. In conclusion, the sRNA-seq based method uses 5' and 3' end small RNAs to annotate nuclear non-coding and mitochondrial genes at 1 bp resolution, and can be used to identify new steady RNAs, particularly long non-coding RNAs (lncRNAs). The high-resolution annotations of mitochondrial genomes can also be used to study the molecular phylogenetics and evolution of animals or to investigate mitochondrial gene transcription, RNA processing, RNA maturation and several other related topics. The complete mitochondrial genome sequence of E. fullo with the new annotations using the sRNA-seq based method is available at the NCBI GenBank database under the accession number MK374364. We publish our theories, methods, the high quality sRNA-seq and RNA-seq data (SRA: SRP174926) for extensive use.

Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5' and 3' End Small RNAs

In this study, we used pan RNA-seq analysis to reveal the ubiquitous existence of both 5′ and 3′ end small RNAs (5′ and 3′ sRNAs). 5′ and 3′ sRNAs alone can be used to annotate nuclear non-coding and mitochondrial genes at 1-bp resolution and identify new steady RNAs, which are usually transcribed from functional genes. Then, we provided a simple and cost effective way for the annotation of nuclear non-coding and mitochondrial genes and the identification of new steady RNAs, particularly long non-coding RNAs (lncRNAs). Using 5′ and 3′ sRNAs, the annotation of human mitochondrial was corrected and a novel ncRNA named non-coding mitochondrial RNA 1 (ncMT1) was reported for the first time in this study. We also found that most of human tRNA genes have downstream lncRNA genes as lncTRS-TGA1-1 and corrected the misunderstanding of them in previous studies. Using 5′, 3′, and intronic sRNAs, we reported for the first time that enzymatic double-stranded RNA (dsRNA) cleavage and RNA interference (RNAi) might be involved in the RNA degradation and gene expression regulation of U1 snRNA in human. We provided a different perspective on the regulation of gene expression in U1 snRNA. We also provided a novel view on cancer and virus-induced diseases, leading to find diagnostics or therapy targets from the ribonuclease III (RNase III) family and its related pathways. Our findings pave the way toward a rediscovery of dsRNA cleavage and RNAi, challenging classical theories.

Evolutionary and functional analysis of Cyclina sinensis c-Jun AP-1 gene in response to LPS stimulation

The transcription factor activator protein-1 (AP-1) plays an essential and critical role in the regulation of numerous downstream genes involved in various physiological and chemical responses. In this study, we identified a full-length cDNA of the c-Jun AP-1 gene (termed Csc-Jun) from the transcriptome library in Cyclina sinensis. The cDNA contains an 825-bp open reading frame that encodes a 274-amino acid protein sequence, including a characteristic Jun transcription factor domain and a highly conserved basic leucine zipper (bZIP) signature that shares 90% identity to that of Ruditapes philippinarum. Furthermore, a phylogenetic analysis using MrBayes and PhyML software (with Bayesian and maximum likelihood approaches, respectively) revealed that the c-Jun AP-1 family genes might be involved in adapting to various environments in different invertebrates. We implemented the PAML software with the maximum likelihood method to further select and verify the positive selection sites (PSSs) in the Mollusca c-Jun AP-1 genes, and we detected four PSSs located in the Jun transcription factor domain. In addition, a spatial expression analysis showed that the Csc-Jun cDNA transcript was ubiquitously expressed in all of the tested tissues and was strongly expressed in the hepatopancreas and weakly expressed in the tissues of the hemocytes, gill filaments, mantle and adductor muscle. Quantitative real-time PCR showed that the expression profiles of Csc-Jun were significantly upregulated at different times in all of the tested tissues when challenged with lipopolysaccharide (LPS). Furthermore, knockdown of Csc-Jun by RNA interference resulted in a higher mortality of C. sinensis following LPS exposure. Finally, we explored the function of the TLR13-MyD88 signaling pathway in the innate immunity of C. sinensis by RNA interference and immune challenges. The results revealed that the mRNA expression levels of Csc-Jun were all decreased (P < 0.01) in normal and stimulated C. sinensis hemocytes. These data collectively indicated that the c-Jun AP-1 gene might play vital roles in innate immunity and provide new evidence for the evolutionary patterns of innate immune genes in Mollusca.

Evolutionary history of a beautiful damselfly, Matrona basilaris, revealed by phylogeographic analyses: the first study of an odonate species in mainland China

Matrona basilaris Selys, 1853 is a damselfly distributed mainly in mainland China. A total of 423 individuals from 48 populations covering almost the entire range were sampled to explore the genetic diversity, phylogeographic structure, and demographic dynamics of the species using sequences of three mitochondrial genes (COI, COII, and ND1) and a nuclear (ITS1 + 5.8 S + ITS2) gene. Phylogenetic tree, median-joining network, and BAPS analyses indicated a four-group division of the entire population, and the divergence event was estimated to have occurred in the middle Pleistocene. The diverse terrain of mainland China as well as past climatic oscillations were assumed to have shaped the current phylogeographic pattern of M. basilaris. Multiple lines of evidence supported population expansion in Group 1 and Group 2 but not in Group 3 or Group 4. The expansion times corresponded to the transition phase from the LIG (∼0.14-0.12 Mya) to the LGM (∼0.021-0.018 Mya). The pre-LGM expansion model reflected a different pattern affecting the historical dynamics of the population of East Asian species caused by Pleistocene climatic changes. Interestingly, Group 2 exhibited a disjunctive distribution pattern. The possible reasons were introgression caused by female-biased dispersal or human phoresy during construction of the Forbidden City during the Ming Dynasty of China.

Complemented Palindromic Small RNAs First Discovered from SARS Coronavirus

In this study, we report for the first time the existence of complemented palindromic small RNAs (cpsRNAs) and propose that cpsRNAs and palindromic small RNAs (psRNAs) constitute a novel class of small RNAs. The first discovered 19-nt cpsRNA UUAACAAGCUUGUUAAAGA, named SARS-CoV-cpsR-19, was detected from a 22-bp DNA complemented palindrome TCTTTAACAAGCTTGTTAAAGA in the severe acute respiratory syndrome coronavirus (SARS-CoV) genome. The phylogenetic analysis supported that this DNA complemented palindrome originated from bat betacoronavirus. The results of RNA interference (RNAi) experiments showed that one 19-nt segment corresponding to SARS-CoV-cpsR-19 significantly induced cell apoptosis. Using this joint analysis of the molecular function and phylogeny, our results suggested that SARS-CoV-cpsR-19 could play a role in SARS-CoV infection or pathogenesis. The discovery of cpsRNAs has paved a way to find novel markers for pathogen detection and to reveal the mechanisms underlying infection or pathogenesis from a different point of view. Researchers can use cpsRNAs to study the infection or pathogenesis of pathogenic viruses when these viruses are not available. The discovery of psRNAs and cpsRNAs, as a novel class of small RNAs, also inspire researchers to investigate DNA palindromes and DNA complemented palindromes with lengths of psRNAs and cpsRNAs in viral genomes.

Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera)

Background

Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. In this study, we sequenced the mt-genomes of five additional Tingidae species and discussed the compositional and mutational rate heterogeneity in mt-genomes and its effect on the phylogenetic inferences of Cimicomorpha by implementing the bias-reduction strategies mentioned above.

Results

Heterogeneity in nucleotide composition and mutational biases were found in mt protein-coding genes, and the third codon exhibited high levels of saturation. Dense taxon sampling of Tingidae and Reduviidae and the other common strategies mentioned above were insufficient to recover the monophyly of the well-established group Cimicomorpha. When the sites with weak phylogenetic signals in the dataset were removed, the remaining dataset of mt-genomes can support the monophyly of Cimicomorpha; this support demonstrates that mt-genomes possess strong phylogenetic signals for the inference of higher-level phylogeny of this group. Comparison of the ratio of the removal of amino acids for each PCG showed that ATP8 has the highest ratio while CO1 has the lowest. This pattern is largely congruent with the evolutionary rate of 13 PCGs that ATP8 represents the highest evolutionary rate, whereas CO1 appears to be the lowest. Notably, the value of Ka/Ks ratios of all PCGs is less than 1, indicating that these genes are likely evolving under purifying selection.

Conclusions

Our results demonstrate that mt-genomes have sites with strong phylogenetic signals for the inference of higher-level phylogeny of Cimicomorpha. Consequently, bioinformatic approaches to removing sites with weak phylogenetic signals in mt-genome without relying on an a priori tree topology would greatly improve this field.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4650-9) contains supplementary material, which is available to authorized users.

Comparative and evolutionary analysis of an adapter molecule MyD88 in invertebrate metazoans

The myeloid differentiation factor 88 (MyD88) is an essential adapter in Toll-like receptor (TLR) signalling pathways, with TLR the first pattern-recognition receptor (PRR) that was discovered in Drosophila. In the present study, a MyD88 gene was identified and characterized from a commercially important shellfish, Scapharca subcrenata, including a DEATH domain and TIR domain conserved within other molluscs. Furthermore, comparative genomic evidence revealed that MyD88 was of different lengths and contained quantitative exon and intron regions, which might be involved in specific mechanisms. To further explore the phylogenetic relationships of invertebrate metazoan MyD88, we applied MrBayes and PhyML software to construct phylogenetic trees using Bayesian and maximum likelihood approaches, respectively, which suggested that the MyD88 of Arthropoda was closely related to lower invertebrates, in contrast to morphological taxonomy. Finally, we investigated the evolutionary patterns and location of positive selection sites (PSSs) in the MyD88 gene from Arthropoda, Mollusca and Insecta using PAML software with the maximum likelihood method. The data showed that positive selection sites were detected in these groups, and partial sites were located in the TIR domain but were not found in the DEATH domain. To summarize, in this study, we report on the diversification of MyD88 in invertebrate metazoans, the specific evolutionary position of Arthropoda MyD88, and the positive selection pressures on MyD88 of Arthropoda, Mollusca and Insecta. These results are a valuable contribution to understand and clarify the evolutionary pattern of TLR/MyD88 signalling pathways in invertebrate and vertebrate taxa.

The TLR13-MyD88-NF-κB signalling pathway of Cyclina sinensis plays vital roles in innate immune responses

Toll-like receptors, the best known pattern recognition receptors, play important roles in recognizing non-self molecules and binding pathogen-associated molecular patterns in the innate immune system. In the present research, the cDNA and protein characterization of the TLR signalling pathway genes including IRAK4, TRAK6 and IKKα (named CsIRAK4, CsTRAF6 and CsIKKα, respectively) with the typical motifs from Cyclina sinensis showed significant similarity with their homologues from other shellfish. Furthermore, the mRNA transcripts of these three genes are ubiquitously expressed in all tissues tested and are dominantly expressed in C. sinensis haemocytes (P < 0.05). Moreover, IRAK4, TRAK6 and IKKα cDNA expression levels were all up-regulated after injection with Vibrio anguillarum, Micrococcus luteus and poly I:C (P < 0.01) as shown by quantitative real-time PCR, indicating that they were involved in responding to pathogenic stimulation. We explored the function of the TLR13-MyD88-NF-κB signalling pathway in the innate immune responses of C. sinensis by RNA interference and immune challenges. The results suggested the mRNA expression patterns of CsMyD88, CsIRAK4, CsTRAF6, CsIKKα, CsIκB, CsNF-κB, CsC-LYZ and CsAMP were all down-regulated (P < 0.01) in normal and stimulated C. sinensis haemocytes, revealing the involvement of the TLR13-MyD88-NF-κB signalling pathway in innate immunity by positively adjusting internal signalling factors and immune-related genes. In summary, a TLR13-MyD88-NF-κB signalling pathway exists and plays vital roles in innate immune responses in C. sinensis. These findings collectively lay the foundation for studying the functional characterization of internal signalling factors and establishing a regulatory network for the TLR signalling pathway in molluscs.