Genetic Distance Analysis Research Articles

First record of Teleogryllus (Brachyteleogryllus) marini Otte & Alexander, 1983 (Orthoptera: Gryllidae) in korea and discussion of its continued misidentification using DNA barcoding

• Teleogryllus (Brachyteleogryllus) marini is newly recorded from Korea. • A key to Korean Teleogryllus species is provided. • T. (B.) marini is transferred to the subgenus Brachyteleogryllus . • Asian T. (B.) marini has been misidentified as T. (B.) commodus with DNA barcoding. DNA barcoding is useful for identifying species that are difficult to distinguish via morphological analysis. However, if the public DNA barcode database includes misidentified DNA samples, subsequent molecular studies could generate incorrect results. Here, we report a misidentified DNA barcode for the North Coastal Black Field Cricket Teleogryllus ( Brachyteleogryllus ) marini . T. (B.) marini is routinely misidentified using DNA barcoding; it has been reported as Teleogryllus (Brachyteleogryllus) commodus since its misidentification in various studies of Asian samples. Here, we report the first occurrence of T. (B.) marini in Korea, along with its morphological diagnosis, bioacoustic signals, and DNA barcoding findings. T. (B.) marini is transferred to the subgenus Brachyteleogryllus from the subgenus Teleogryllus , based on the male genitalia morphology and phylogenetic analysis. Genetic distance analyses have shown that cytochrome c oxidase I barcoding is useful for species identification of the genus Teleogryllus, but detailed morphological investigations are essential for DNA barcoding before any molecular study.

Net-Winged Midge Genus Blepharicera Macquart (Diptera: Blephariceridae) in China: The First DNA Barcode Database with Descriptions of Four New Species and Notes on Distribution.

Simple SummaryBlephariceridae is a small but highly specialized family in Diptera with extreme morphological adaptations for living in fast-moving waters. Among the seven blepharicerid genera in China, Blepharicera Macquart, 1843 is the species richest genus with 12 known species. There is a serious gap in knowledge concerning larval stages and connecting them to adult morphology. At present, DNA barcoding using mitochondrial (mt) cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for identification in many animal groups. There are about 60 species of the genus Blepharicera known in the world. However, only one identified Blepharicera species from Europe is currently available in DNA sequence repositories, and a DNA barcode database is still lacking for Chinese Blepharicera. To fill this gap, we started a project with the objectives to collect specimens of Blepharicera across China, identify the species by morphological characters, and build an mt COI barcode database for this important insect group. Molecular and morphological markers show that four morphospecies examined represent members of the genus Blepharicera and constitute four new, distinct species. This initial attempt indicates the validity of mt COI barcodes for Blepharicera in delimiting species and contributes to the growing library of DNA barcodes of net-winged midges of the world.Mitochondrial (mt) cytochrome c oxidase 1 (COI) gene is more and more widely used for DNA barcoding, which provides a rapid and timely identification as this technique is not limited by polymorphism, sex, and life stages and fundamentally complements traditional evolutionary taxonomy. The present study generated 33 mt COI sequences of seven Chinese Blepharicera Macquart, 1843 species with an average of 594 bp, which represent the first DNA barcode database for Chinese Blepharicera. Genetic distance analysis reveals that intraspecific distances in the genus are generally less than 1.7%, and interspecific distances range from 5.4% to 20.3%. Phylogenetic analysis shows that each species recovered in our analyses is separated from all neighboring species. Based on molecular and morphological data, four Blepharicera species from China, B. beishanica sp. nov., B. dushanzica sp. nov., B. nigra sp. nov. and B. xinjiangica sp. nov., are described and illustrated as new to science. Identification keys for adults and larvae of Chinese Blepharicera are also presented. Geographical analysis shows that Southwest China is the species’ richest region. Our results will be useful in tackling taxonomic problems, understanding species distribution, and resolving nomenclature conflicts associated with Blepharicera species.

Undiagnosed HIV Infections May Drive HIV Transmission in the Era of "Treat All": A Deep-Sampling Molecular Network Study in Northeast China during 2016 to 2019.

Universal antiretroviral therapy (ART, “treat all”) was recommended by the World Health Organization in 2015; however, HIV-1 transmission is still ongoing. This study characterizes the drivers of HIV transmission in the “treat all” era. Demographic and clinical information and HIV pol gene were collected from all newly diagnosed cases in Shenyang, the largest city in Northeast China, during 2016 to 2019. Molecular networks were constructed based on genetic distance and logistic regression analysis was used to assess potential transmission source characteristics. The cumulative ART coverage in Shenyang increased significantly from 77.0% (485/630) in 2016 to 93.0% (2598/2794) in 2019 (p < 0.001). Molecular networks showed that recent HIV infections linked to untreated individuals decreased from 61.6% in 2017 to 28.9% in 2019, while linking to individuals with viral suppression (VS) increased from 9.0% to 49.0% during the same time frame (p < 0.001). Undiagnosed people living with HIV (PLWH) hidden behind the links between index cases and individuals with VS were likely to be male, younger than 25 years of age, with Manchu nationality (p < 0.05). HIV transmission has declined significantly in the era of “treat all”. Undiagnosed PLWH may drive HIV transmission and should be the target for early detection and intervention.

Testing the effectiveness of rbcLa DNA-barcoding for species discrimination in tropical montane cloud forest vascular plants (Oaxaca, Mexico) using BLAST, genetic distance, and tree-based methods.

DNA-barcoding is a species identification tool that uses a short section of the genome that provides a genetic signature of the species. The main advantage of this novel technique is that it requires a small sample of tissue from the tested organism. In most animal groups, this technique is very effective. However, in plants, the recommended standard markers, such as rbcLa, may not always work, and their efficacy remains to be tested in many plant groups, particularly from the Neotropical region. We examined the discriminating power of rbcLa in 55 tropical cloud forest vascular plant species from 38 families (Oaxaca, Mexico). We followed the CBOL criteria using BLASTn, genetic distance, and monophyly tree-based analyses (neighbor-joining, NJ, maximum likelihood, ML, and Bayesian inference, BI). rbcLa universal primers amplified 69.0% of the samples and yielded 91.3% bi-directional sequences. Sixty-three new rbcLa sequences were established. BLAST discriminates 80.8% of the genus but only 15.4% of the species. There was nil minimum interspecific genetic distances in Quercus, Oreopanax, and Daphnopsis. Contrastingly, Ericaceae (5.6%), Euphorbiaceae (4.6%), and Asteraceae (3.3%) species displayed the highest within-family genetic distances. According to the most recent angiosperm classification, NJ and ML trees successfully resolved (100%) monophyletic species. ML trees showed the highest mean branch support value (87.3%). Only NJ and ML trees could successfully discriminate Quercus species belonging to different subsections: Quercus martinezii (white oaks) from Q. callophylla and Q. laurina (red oaks). The ML topology could distinguish species in the Solanaceae clade with similar BLAST matches. Also, the BI topology showed a polytomy in this clade, and the NJ tree displayed low-support values. We do not recommend genetic-distance approaches for species discrimination. Severe shortages of rbcLa sequences in public databases of neotropical species hindered effective BLAST comparisons. Instead, ML tree-based analysis displays the highest species discrimination among the tree-based analyses. With the ML topology in selected genera, rbcLa helped distinguish infra-generic taxonomic categories, such as subsections, grouping affine species within the same genus, and discriminating species. Since the ML phylogenetic tree could discriminate 48 species out of our 55 studied species, we recommend this approach to resolve tropical montane cloud forest species using rbcLa, as an initial step and improve DNA amplification methods.

MORPHOMETRY OF FIRST-STAGE LARVAE OF ORTHOSTRONGYLUS MACROTIS (NEMATODA: PROTOSTRONGYLIDAE), LUNGWORM OF WILD UNGULATES FROM WESTERN NORTH AMERICA.

Orthostrongylus macrotis (Dikmans, 1931) is a protostrongylid lungworm in wild ungulates from western North America, including mule and Columbia black-tailed deer, pronghorn, and rarely moose and elk. The lack of morphological data for certain developmental stages of O. macrotis and the unresolved taxonomic status of the genus indicate a more detailed morphological characterization of the species is necessary. We provide a detailed description of first-stage larvae (L1) of O. macrotis including morphological, morphometric, and molecular data. Species identity was confirmed based on molecular sequence data from the internal transcribed spacer subunit 2 (ITS-2) and large subunit (28S) rDNA. A fragment of the cytochrome oxidase c subunit 1 (COI) was also sequenced, followed by the determination of genetic distance and phylogenetic analyses. Integrated data describing L1 of O. macrotis contributes to a broader understanding of the parasite fauna of wild ungulates from North America and may be of relevance for a future revision of the genus. Further, we outline information for differentiation among species of North American protostrongylids, with typical spike-tailed L1s, circulating among free-ranging and semi-domestic ungulates.

Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat.

Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.

Resolving the phylogenetic relationship betweenParmotrema crinitumandParmotrema perlatumpopulations

AbstractThe widespread speciesParmotrema crinitum(Ach.) M. Choisy andParmotrema perlatum(Huds.) M. Choisy are mainly distinguished by their reproductive strategies. WhileP. crinitumpropagates by isidia,P. perlatumproduces soredia. In this study, we aim to evaluate the phylogenetic relationship between both species and to critically examine their species boundaries. To this purpose, 46 samples belonging toP. crinitumandP. perlatumwere used in our analysis, including 22 for which we studied the morphology and chemistry, before extracting their DNA. We used 35 sequences of the internal transcribed spacer region of nuclear ribosomal DNA (ITS) ofParmotrema perlatumfrom Europe and Africa (20 of which were newly generated), and 11 ofParmotrema crinitumfrom Europe, North America and North Africa (two newly generated). Additionally, 28 sequences of several species fromParmotremawere included in the ITS dataset. The ITS data matrix was analyzed using different approaches, such as traditional phylogeny (maximum likelihood and Bayesian analyses), genetic distances, automatic barcode gap discovery (ABGD) and the coalescent-based method poisson tree processes (PTP), in order to test congruence among results. Our results indicate that all samples referred toP. crinitumandP. perlatumnested in a well-supported monophyletic clade, but phylogenetic relationships among them remain unresolved. Delimitations inferred from PTP, ABGD and genetic distance analyses were comparable and suggested thatP. crinitumandP. perlatumbelong to the same lineage. Interestingly, two samples ofP. perlatumseparate in a different monophyletic clade, which is supported as a different lineage by all the analyses.

MOLECULAR CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF THE NATIVE SMALL CARPENTER BEES (CERATINA SPP.) OF NORTH WESTERN, INDIAN HIMALAYAS

Bees are a wonderful creatures on earth; contributing to 73% of pollination services provided byall animals. Although the economic value of domesticated bees is calculated through several scientificmethods, but the actual value of wild bees in terms of economy, ecology and biodiversity are rarelyestimated due to lack of distinct taxonomic keys. Considering the above backdrops, we decided tomolecularly characterize three species of Ceratina native to Indian Himalayas. Three species were reportedas C. sutepensis, C. smaragdula and C. similima based on phylogenetic analysis and comparison with the NCBIdatabase. The COI sequence of C. similima was submitted to the NCBI database for the first time. Nucleotidefrequency analysis showed that partial COI gene sequences were A+T biased (&gt;75%), while the amino acidfrequency analysis showed higher frequency of leucine (16.01%) and serine (11.77%). Multiple sequencealignment of COI sequences of three species illustrated the total variation in 117 SNP’s. Moreover, thepairwise genetic distance analysis reported that C. sutepensis and C.smaragdulawere genetically less distantwhen compared toC. similima. Suchkinds of studies are essential to analyze the biodiversity of location,distinguish cryptic species and develop distinct taxonomic tools for integrative taxonomy of bees.

Prehistoric Human Forensic DNA Analysis From Lore Highlands, Central Sulawesi With Present Day Human DNA

Mitochondrial DNA or mtDNA(s) are inherited maternally, in other words they can only be inherited through females in a family, which makes them frequently used in forensic studies. In this research, the Hypervariable-I part (HV-1) in the D-Loop region of the ancient forensic samples acquired from Lore Highlands will be compared with present day human DNA from the same region. The steps conducted in this research includes DNA extraction, mtDNA amplification with specific primers, sequencing, and phylogenetic analysis. The analysis were done between 4 ancient forensic samples; A, B, G, and J, and 33 comparison sequences from GenBank, including ancient forensic sample acquired from Tadulako site, Lore Highlands, from previous research. The result of genetic distance analysis showed that the distance between 37 samples were very close; with difference ranging from 0,02% - 0,13%. The analysis also gives a clue about Austronesian relation with Australomelanesian. The result from phylogenetic tree reconstructions (maximum-likelihood and neighbor-joining) showed little differences. However, there is a small significant difference detected from the neighbour-joining tree construction result and will be discussed further in this paper.

Identifikasi Genetik Udang Mantis Dengan Pendekatan DNA Barcoding Gen Sitokrom Oksidase 1 (CO1)

Mantis shrimp is one of the marine organisms that has a very abundant diversity of species. The similarity of morphology of this group make it difficult to identify morphologically. Therefore, identification was carried out using a DNA barcoding approach. The purpose of this study was to identify the mantis shrimp species from Manokwari waters using molecular techniques. The CO1 gene fragments were amplified by using LCO and HCO primers. The DNA sequences obtained were analyzed for homology, phylogeny, and genetic distance using MEGA X software. A total of 537 base pairs of CO1 gene fragments of mantis shrimp from Manokwari were obtained. The results of the homology analysis on GenBank, show the highest similarity of 91.18% with sequences from the genus Gonodactylus. Analysis of phylogenetic tree and genetic distance showed the same results and supported each other with homology analysis on GenBank data.

Mitochondrial COI sequences revealed shallow but significant divergences among Amphioctopus aegina (Octopoda, Octopodidae) populations in coastal waters of China

Amphioctopus aegina is an important fishery resource in the coastal waters of China. In the present study, the genetic diversity and population genetic structure among four populations of A. aegina throughout its distributional range in China were assessed using the mitochondrial cytochrome oxidase 1 (COI) sequences. The results revealed a generally low genetic diversity (Hd: 0.2842–0.6670; Pi: 0.0007–0.0015) in A. aegina populations. The neighbor-joining (NJ) phylogenetic tree and the haplotype networks, as well as the results of the molecular variance (AMOVA) analyses, indicated a shallow phylogeographic structure among the four populations. However, pairwise ΦST statistics and genetic distance analyses revealed significant (p&lt;0.01) genetic differentiation among Qinzhou and the rest three populations of Zhanjiang, Huizhou, and Dongshan. The demographic history analyses indicated a population expansion in A. aegina, and the role of Leizhou peninsula isolation in shaping the population differentiation. These results would largely enhance our understanding of the genetic structure and hence promote the scientific management of A. aegina fishery resources in coastal waters of China.

Rapid evaluation of COVID-19 vaccine effectiveness against symptomatic infection with SARS-CoV-2 variants by analysis of genetic distance

Timely evaluation of the protective effects of Coronavirus Disease 2019 (COVID-19) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is urgently needed to inform pandemic control planning. Based on 78 vaccine efficacy or effectiveness (VE) data from 49 studies and 1,984,241 SARS-CoV-2 sequences collected from 31 regions, we analyzed the relationship between genetic distance (GD) of circulating viruses against the vaccine strain and VE against symptomatic infection. We found that the GD of the receptor-binding domain of the SARS-CoV-2 spike protein is highly predictive of vaccine protection and accounted for 86.3% (P = 0.038) of the VE change in a vaccine platform-based mixed-effects model and 87.9% (P = 0.006) in a manufacturer-based model. We applied the VE-GD model to predict protection mediated by existing vaccines against new genetic variants and validated the results by published real-world and clinical trial data, finding high concordance of predicted VE with observed VE. We estimated the VE against the Delta variant to be 82.8% (95% prediction interval: 68.7–96.0) using the mRNA vaccine platform, closely matching the reported VE of 83.0% from an observational study. Among the four sublineages of Omicron, the predicted VE varied between 11.9% and 33.3%, with the highest VE predicted against BA.1 and the lowest against BA.2, using the mRNA vaccine platform. The VE-GD framework enables predictions of vaccine protection in real time and offers a rapid evaluation method against novel variants that may inform vaccine deployment and public health responses.

Exploring the Genetic Diversity and Population Structure of Wheat Landrace Population Conserved at ICARDA Genebank.

Landraces are considered a valuable source of potential genetic diversity that could be used in the selection process in any plant breeding program. Here, we assembled a population of 600 bread wheat landraces collected from eight different countries, conserved at the ICARDA's genebank, and evaluated the genetic diversity and the population structure of the landraces using single nucleotide polymorphism (SNP) markers. A total of 11,830 high-quality SNPs distributed across the genomes A (40.5%), B (45.9%), and D (13.6%) were used for the final analysis. The population structure analysis was evaluated using the model-based method (STRUCTURE) and distance-based methods [discriminant analysis of principal components (DAPC) and principal component analysis (PCA)]. The STRUCTURE method grouped the landraces into two major clusters, with the landraces from Syria and Turkey forming two clusters with high proportions of admixture, whereas the DAPC and PCA analysis grouped the population into three subpopulations mostly according to the geographical information of the landraces, i.e., Syria, Iran, and Turkey with admixture. The analysis of molecular variance revealed that the majority of the variation was due to genetic differences within the populations as compared with between subpopulations, and it was the same for both the cluster-based and distance-based methods. Genetic distance analysis was also studied to estimate the differences between the landraces from different countries, and it was observed that the maximum genetic distance (0.389) was between the landraces from Spain and Palestine, whereas the minimum genetic distance (0.013) was observed between the landraces from Syria and Turkey. It was concluded from the study that the model-based methods (DAPC and PCA) could dissect the population structure more precisely when compared with the STRUCTURE method. The population structure and genetic diversity analysis of the bread wheat landraces presented here highlight the complex genetic architecture of the landraces native to the Fertile Crescent region. The results of this study provide useful information for the genetic improvement of hexaploid wheat and facilitate the use of landraces in wheat breeding programs.

Gamma Radiation (60Co) Induces Mutation during In Vitro Multiplication of Vanilla (Vanilla planifolia Jacks. ex Andrews)

In vitro mutagenesis is an alternative to induce genetic variation in vanilla (Vanilla planifolia Jacks. ex Andrews), which is characterized by low genetic diversity. The objective of this study was to induce somaclonal variation in V. planifolia by gamma radiation and detect it using inter-simple sequence repeat (ISSR) molecular markers. Shoots previously established in vitro were multiplied in Murashige and Skoog culture medium supplemented with 2 mg·L−1 BAP (6-benzylaminopurine). Explants were irradiated with different doses (0, 20, 40, 60, 80 and 100 Gy) of 60Co gamma rays. Survival percentage, number of shoots per explant, shoot length, number of leaves per shoot, and lethal dose (LD50) were recorded after 60 d of culture. For molecular analysis, ten shoots were used for each dose and the donor plant as a control. Eight ISSR primers were selected, and 43 fragments were obtained. The percentage of polymorphism (% P) was estimated. A dendrogram based on Jaccard’s coefficient and the neighbor joining clustering method was obtained. Results showed a hormetic effect on the explants, promoting development at low dose (20 Gy) and inhibition and death at high doses (60–100 Gy). The LD50 was observed at the 60 Gy. Primers UBC-808, UBC-836 and UBC-840 showed the highest % P, with 42.6%, 34.7% and 28.7%, respectively. Genetic distance analysis showed that treatments without irradiation and with irradiation presented somaclonal variation. The use of gamma rays during in vitro culture is an alternative to broaden genetic diversity for vanilla breeding.

Isolasi dan Karakterisasi Molekuler Gen 16S rRNA Bakteri Lipolitik Asal Limbah Kulit Biji Jambu Mete

Lipolytic bacteria attract great attention to various biotechnology industries because of their enzymatic potential. This study aims to isolate and identify lipolytic bacteria from cashew nutshell waste using the 16S rRNA gene as a molecular marker. Lipolytic bacteria were isolated using serial dilutions and inoculated on lipolytic media. A total of 3 isolates of lipolytic bacteria were obtained from cashew nutshell waste based on screening in LA Rhodamine B. The partial sequence of 16S rRNA gene from LB15 amplified using a pair of primers 63F and 1387R having a size of 1238 bp, while BL6 and BK6 were 1283 bp, respectively. Based on genetic distance analysis and phylogenetic reconstruction, we proposed that LB15 be identified as Burkholderia sp. with 99.92% similarity. In addition, because the 16S rRNA gene sequence similarity of BL6 was 99.87% with Paraburkholderia kururiensis strain 979, BL6 was classified as Paraburkholderia kururiensis. Then, isolate BK6 was identified as Ralstonia sp. with a similarity of 99.53%. The similarity value can be used as a reference in determining the identity of bacteria. A bacterium can be categorized as the same species if it has a similarity value of more than 99%.&#x0D;

Population connectivity and genetic diversity population connectivity of Rabbitfish (Siganus canaliculatus) among Bangladesh, China and Indonesia

Population genetics studies genetic variation involving gene and allele frequencies in spatial and temporal space. Genetic information can be used in conservation management through identification of phylogenetic tree reconstructions, genetic distance, genetic structure, and haplotype connectivity to maintain population existence. The samples used were primary genetic data of Siganus canaliculatus taken from Indonesian waters and secondary data accessed from the BOLD SYSTEM database from several locations, namely Indonesia, China, and Bangladesh. This research was conducted to determine the kinship of Siganus canaliculatus in Indonesia, China, and Bangladesh through genetic analysis. The results of genetic distance analysis showed that the baronang fish samples from China and Bangladesh had a close relationship with a value of 0.0534 while samples from Indonesia and Bangladesh had the farthest relationship with a value of 0.8212. Reconstruction of the phylogeny tree at maximum likelihood can show convergence within the same clade. The results of the reconstruction of the phylogeny tree showed that the species from Ambon, Bali, and Lombok came from the same clade while samples from Bangladesh had different clades with the furthest distance. The results of structural analysis and genetic diversity showed that samples from Bangladesh, China, and Indonesia had different DNA characteristics. This is correlated with the form of network integration in haplotype connectivity analysis.

Partial redescriptions of three holothurians with hook papillae (Apodida: Chiridotidae): Taeniogyrus japonicus (Marenzeller, 1882), T. dendyi (Mortensen, 1925), Scoliorhapis theelii (Heding, 1928).

New specimens of Taeniogyrus japonicus (Marenzeller) were collected from Iwami coast and Sado island of the Sea of Japan. According to detailed observations of external and internal organs, we transferred T. japonicus, T. dendyi (Mortensen), and Scoliorhapis theelii (Heding) to the newly revived genus Scoliodota, with a large retractor organ and hook papillae as major diagnostic characters. We also concluded that Scoliorhapis dianthus Solis-marin et al. is a synonym of T. japonicus. Our molecular phylogeny and genetic distance analysis showed that specimens from Iwami and specimens from Sado of T. japonicus form a monophyletic clade, indicating that they are most likely the same species despite their morphological variation. The phylogenetic analysis also indicated that T. japonicus forms a sister group relationship with Taeniogyrus verruculosus Yamana Tanaka and Scoliorhapis sesokoensis Yamana Tanaka, suggesting that Taeniogyrus is not monophyletic. Taken together, these results brought new insights to sea cucumber diversity in Japanese waters.

Identification of a new nucleopolyhedrovirus isolated from the olive leaf moth, Palpita vitrealis, from two locations in Egypt

The olive leaf moth (jasmine moth), Palpita vitrealis (Lepidoptera: Crambidae), is an important insect pest of olives in several Mediterranean countries. A new alphabaculovirus was isolated from diseased larvae of P. vitrealis in Egypt, first in Giza in spring 2005 and again in Marsa Matrouh in 2019.The larvae exhibited typical symptoms of a baculovirus infection. Light and scanning electron microscopy studies revealed polyhedral occlusion bodies. Transmission electron microscopy of ultrathin sections of purified OBs revealed virions with multiple embedded nucleocapsids. The identity of the two virus isolates was confirmed by sequencing the partial polyhedrin and lef-8 genes, and sequence comparison suggested a relationship to group I alphabaculoviruses. Therefore, this virus was termed Palpita vitrealis nucleopolyhedrovirus (PaviNPV). Whole genome sequencing of the PaviNPV isolate from Giza (Gz05) revealed a genome of 117,533 bp, 131 open reading frames (ORFs) and four homologous repeat (hr) regions. Phylogenetic reconstruction and genetic distance analyses using 38 core genes indicated that PaviNPV should be considered to belong to a novel species within the genus Alphabaculovirus. In bioassays, PaviNPV was highly virulent against second-instar larvae of P. vitrealis. The study reports a novel baculovirus that might have potential as a biological control agent of the olive leaf moth.

A new species of the genus Pseudohampsonella Solovyev amp; Saldaitis (Lepidoptera: Limacodidae) from Xizang Autonomous Region, China.

The sixth species of the genus Pseudohampsonella Solovyev Saldaitis, 2014, P. medogensis sp. nov., is described from Xizang Autonomous Region, China. The new species is morphologically similar to the congeners P. bayizhena Wu Pan, 2015 and P. hoenei Solovyev Saldaitis, 2014, but differs from them by the uncus slightly waved with a blunt apex and the phallus distinctly curved mesally. Images of adults and genitalia are presented. The circumscription of the new species is supported molecularly by the analysis of the pairwise genetic distances using mitochondrial cytochrome c oxidase subunit I (COI) gene. The minimum interspecific distance value between the new species and its sister species, P. lii Wang Li, 2017, is 7.7%.

Development of SSR markers and genetic diversity analysis based on RAD-seq technology among Chinese populations of Daphnia magna.

Daphnia magna belongs to the Cladocera order and plays an important role in the aquatic ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. 26 novel microsatellite (SSR) markers were developed in an artificially domesticated D. magna and 12 wild D. magna populations using restriction site-associated DNA sequencing (RAD-seq). The results showed that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.083 to 0.999 and 0.085 to 0.862, respectively. The PIC ranged from 0.368 to 0.805. These results indicate that the developed SSR marker is highly polymorphic. Nei's genetic identity (H) ranged from 0.0926 to 0.3462. Shannon's Information index (I) ranged from 0.1333 to 0.4799. Genetic distance and Nei's genetic identity analysis, NJ tree diagram analysis, and PCoA analysis were conducted on populations of D. magna from different regions. The results show that the D. magna genetic relationship between Liaoning and Shanxi, Hunan and Anhui, and Beijing and Hainan are relatively close, while the genetic structure of D. magna in Guangdong, Jiangsu, and Sichuan is quite different from other sampling sites. An analysis of population genetic structure divided the D. magna samples into two major groups. These results indicate that the genetic structure of D. magna differs considerably in different regions. Our research results and the newly developed polymorphic SSR markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated populations and conservation genetics research.