Sequence Comparison Research Articles

Transcriptome profiling uncovers differentially expressed genes linked to nutritional quality in vegetable soybean.

Vegetative soybean (maodou or edamame) serves as a nutrient-rich food source with significant potential for mitigating global nutritional deficiencies. This study undertook a thorough examination of the nutritional profiles and transcriptomic landscapes of six soybean cultivars, including three common cultivars (Heinong551, Heinong562, and Heinong63) and three fresh maodou cultivars (Heinong527, HeinongXS4, and HeinongXS5). Nutrient analysis of the seeds disclosed notable differences in the levels of protein, fat, soluble sugars, vitamin E, calcium, potassium, magnesium, manganese, iron, and zinc across the cultivars. Through comparative transcriptome profiling and RNA sequencing, distinct variations in differentially expressed genes (DEGs) were identified between fresh and traditional maodou cultivars. Functional enrichment analyses underscored the involvement of DEGs in critical biological processes, such as nutrient biosynthesis, seed development, and stress responses. Additionally, association studies demonstrated robust correlations between specific DEG expression patterns and seed nutrient compositions across the different cultivars. Sankey diagrams illustrated that DEGs are strongly linked with seed quality traits, revealing potential molecular determinants that govern variations in nutritional content. The identified DEGs and their relationships with nutritional profiles offer valuable insights for breeding programs focused on developing cultivars with improved nutritional quality, tailored to specific dietary needs or industrial applications.

VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences.

The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable, universal, and automated preliminary taxonomic framework for comprehensive virus studies. Here, we introduce VISTA (Virus Sequence-based Taxonomy Assignment), a computational tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for virus taxonomy. Leveraging physio-chemical property sequences, k-mer profiles, and machine learning techniques, VISTA constructs a robust distance-based framework for taxonomic assignment. Functionally similar to PASC (Pairwise Sequence Comparison), a widely used virus assignment tool based on pairwise sequence comparison, VISTA demonstrates superior performance by providing significantly improved separation for taxonomic groups, more objective taxonomic demarcation thresholds, greatly enhanced speed, and a wider application scope. We successfully applied VISTA to 38 virus families, as well as to the class Caudoviricetes. This demonstrates VISTA's scalability, robustness, and ability to automatically and accurately assign taxonomy to both prokaryotic and eukaryotic viruses. Furthermore, the application of VISTA to 679 unclassified prokaryotic virus genomes recovered from metagenomic data identified 46 novel virus families. VISTA is available as both a command line tool and a user-friendly web portal at https://ngdc.cncb.ac.cn/vista.

New vouchered and taxonomically verified records of cave-dwelling populations of catfishes of the genus Rhamdia (Siluriformes, Heptapteridae) from Costa Rica

Dedicated ichthyological surveys in two karstic caves in Costa Rica resulted in the discovery of hypogean populations from three epigean species of catfishes of the genus Rhamdia. The taxonomic identity of these populations was initially determined based on morphological traits and subsequently corroborated with comparative DNA sequence data in a phylogenetic framework. Individuals from all hypogean populations documented herein exhibit only partial troglomorphism, characterized by only moderate (vs. complete) integumentary depigmentation without extreme eye reduction/loss. A similar pattern of incomplete troglomorphism at the individual level has been observed in other cave-dwelling species/populations of Middle American Rhamdia, and tentatively attributed to gene flow with and/or incipient speciation from epigean lineages. Since most hypogean forms of Rhamdia derive from/are part of a larger clade of primarily R. laticauda, our discovery of cave-dwelling populations assignable to R. nicaraguensis and R. guatemalensis is noteworthy, particularly in the case of the former, which represents the first taxonomically verified record of a cave-dwelling population of this epigean species. Among our findings is the remarkable discovery of hypogean populations from two different species of Rhamdia (R. laticauda and R. nicaraguensis) inhabiting the same cave (Gabinarraca). This finding is particularly significant because it represents the first time that cave-dwelling populations from different species of Rhamdia are reported to be living in syntopy. Continued discovery of cave-dwelling populations during targeted ichthyological surveys reinforces the notion that our understanding of the diversity of hypogean Rhamdia is incomplete and that sustained exploration and taxonomically sound documentation work are paramount to advancing knowledge about the diversity and evolution of these group of Neotropical catfishes.

Comprehensive genome analysis of two novel Saccharopolyspora strains—Saccharopolyspora montiporae sp. nov. and Saccharopolyspora galaxeae sp. nov. isolated from stony corals in Hainan

Marine actinomycetes exhibit a high level of biodiversity and possess significant potential for the production of high-value secondary metabolites. During the course of investigation of marine actinobacteria from corals, two Saccharopolyspora strains, namely, HNM0983T and HNM0986T, were isolated from stony corals collected from the coastal area of Hainan Island. The 16S ribosomal RNA (rRNA) gene sequence analysis revealed that these two strains are putative novel taxa of the genus Saccharopolyspora. Whole-genome sequencing comparisons further confirmed the two strains as belonging to two novel Saccharopolyspora species, which can be distinguished phenotypically and chemically from their current closest phylogenetic relatives. Some genomic information of the genus Saccharopolyspora was compared for evaluating the production capacity of secondary metabolites. A total of 519 biosynthetic gene clusters (BGCs) from the genus Saccharopolyspora were used for analysis, and terpene BGCs were found to be widespread and most abundant in this genus. In addition, abundant novel BGCs in the genus Saccharopolyspora are not clustered with the known BGCs in the database, indicating that the metabolites of the genus Saccharopolyspora deserve further exploration. On the basis of these presented results, Saccharopolyspora montiporae sp. nov. (type strain = HNM0983T = CCTCC AA 2020014T = KCTC 49526T) and Saccharopolyspora galaxeae sp. nov. (type strain = HNM0986T = CCTCC AA 2020011T = KCTC 49524T) are proposed as the names for the new strains, respectively.

Chalaropsis pruni sp. nov. (Ceratocystidaceae), a new species from Prunus serrulata var. pubescens in South Korea

A routine survey in a natural forest located in the Gangwon Province of Korea was undertaken in 2022 to establish an inventory of potentially pathogenic fungi that might affect tree health in the country. An ophiostomatoid fungus was consistently isolated from naturally occurring wounds on Prunus serrulata var. pubescens. Isolates were subjected to morphological and DNA sequence comparisons. The results showed that the fungus resided in a distinct taxonomic lineage, and the novel species is described here as Chalaropsis pruni sp. nov.

Comparison of rDNA-ITS Sequences, Vegetative Compatibility, Biological Characteristics, and Thifluzamide Sensitivity of Rhizoctonia solani AG-3 PT, TM, and TB Subgroup Isolates Collected from Potato and Tobacco in China.

Potato black scurf and tobacco target spot are significant agricultural diseases primarily caused by Rhizoctonia solani AG-3, which is further classified into PT (potato type), TM (tomato type), and TB (tobacco type) subgroups, with the naming of these subgroups originally indicating their respective infection hosts potato, tomato, and tobacco. This study determined the subgroup classification of 129 R. solani AG-3 isolates recovered from tobacco leaves exhibiting target spot disease in major tobacco-cultivating regions of China, as well as 80 R. solani AG-3 isolates obtained from potato stem cankers and tuber sclerotia in Liaoning, Jilin, and Heilongjiang provinces, and Inner Mongolia autonomous region of China. Sequence analysis of the internal transcribed spacer (ITS) regions revealed that all potato isolates belonged to the R. solani AG-3 PT subgroup, whereas the tobacco isolates were classified into TM and TB subgroups. Specifically, 51 strains from the northeast (Liaoning, Jilin, and Heilongjiang provinces) belonged to the TM subgroup, while the others belonged to the TB subgroup. Phylogenetic analysis indicated a closer relationship between AG-3 TM and AG-3 PT compared to AG-3 TB. Population genetic analysis highlighted distinct genetic variations among the subgroups, with the AG-3 TB subgroup isolates exhibiting fewer ITS1 variable sites and the AG-3 PT subgroup displaying a higher number of ITS2 variable sites. Furthermore, comparisons were made regarding macroscopic vegetative interactions, biological characteristics, pathogenicity to potato and tobacco, and susceptibility to thifluzamide among the three subgroups. The results indicated no macroscopic somatic interactions among the subgroups, with the highest frequency of somatic incompatibility observed within AG-3 PT, followed by AG-3 TM, and AG-3 TB. Additionally, the three subgroups differed in colony color, sclerotium morphology, production time, and distribution location on potato-dextrose-agar (PDA) medium, with AG-3 TM being the least likely to produce sclerotia. Regarding temperature, optimal growth conditions varied among the subgroups. Regarding pathogenicity, the AG-3 PT subgroup strains were more pathogenic on tobacco and potato stem bases compared to the AG-3 TB subgroup, whereas the AG-3 TB and TM subgroup strains were more pathogenic on leaves. Notably, AG-3 TM exhibited remarkable virulence towards both the stem base and leaves. The AG-3 PT subgroup strains exhibited the highest susceptibility to thifluzamide, with a susceptibility baseline of 0.037±0.013 mg·L-1, followed by the AG-3 TM subgroup strains with a baseline of 0.111±0.034 mg·L-1, and the AG-3 TB subgroup strains with a baseline of 0.137±0.035 mg·L-1. This study contributes to a deeper understanding of the biology and etiology of the three subgroups of R. solani AG-3, providing a valuable theoretical basis for the scientific control and management of tobacco target spot and potato black scurf diseases in China.

BIOM-22. SPATIAL, SINGLE-CELL, AND BULK RNA SEQUENCING IDENTIFY MOLECULAR PROGRAMS UNDERLYING MENINGIOMA BRAIN INVASION

Abstract Brain invasion is a negative prognostic factor for meningiomas, but the molecular programs underlying meningioma brain invasion are poorly understood. To address this, we performed transcriptomic analyses of 3 independent datasets: Bulk RNA sequencing from 199 meningiomas (n=33 with brain invasion), single-cell RNA sequencing of 2 regionally distinct samples from the brain tumor interface (BTI) versus tumor core (TC) (n=22,118 single-cell transcriptomes), and spatial RNA sequencing from 6 samples with (n=4) versus without (n=2) brain invasion (n=18,471 spatial transcriptomes). Single-cell and spatial datasets were integrated with Harmony, cell interactions were defined using CellChat, and cross-platform comparisons were performed with the Seurat data integration pipeline. Bulk RNA sequencing revealed enrichment of 1835 genes in meningiomas with brain invasion compared to those without brain invasion, including glial markers (GFAP, NCAN) and markers of extracellular matrix remodeling (PDGFRA, COL9A1). Single-cell RNA sequencing comparison of BTI versus TC meningioma cells identified 2793 genes that were enriched in BTI cells, 268 of which were conserved across bulk and single-cell transcriptomes from brain-invasive meningiomas. Gene ontology enrichment analysis showed molecular programs underlying cell migration and regulation of neurogenesis at the BTI, while glycolysis and antigen presentation programs were enriched in the TC. Cholesterol, CSPG4, and LIF signaling were active in the TC, while SLIT signaling was enriched at the BTI. Spatial RNA sequencing showed enrichment of 439 genes at the BTI, and a conserved set of 12 genes were enriched in BTI meningioma cells across bulk, single-cell, and spatial datasets (TGM2, APOC1, IGFBP6, PLEKHO1, GFPT2, ZYX, IQGAP3, LUM, S100A11, ARPC1B, CDK1, CYCS). Comparison of tumor microenvironment monocytes at the BTI versus TC demonstrated enrichment of 1571 genes that were associated with macrophage migration and activation. These data elucidate molecular programs underlying meningioma brain invasion and provide insights into meningioma intratumor heterogeneity.

Molecular characterization of a novel partitivirus with four segments isolated from Fusarium solani, the causal agent of citrus root rot.

We report here the identification of a dsRNA virus, obtained from Fusarium solani strain Newher-7, tentatively named F. solani partitivirus 3 (FsPV3). It consists of four dsRNA segments (dsRNA1-4) with lengths of 1961, 1900, 1830 and 1830 bp, respectively. Sequence analysis showed that dsRNA1 encodes an RNA-dependent RNA polymerase (RdRp), dsRNA2 encodes a capsid protein (CP), dsRNA3 encodes a hypothetical protein of unknown function and dsRNA4 encodes two hypothetical proteins of unknown function. Amino acid sequence comparisons showed that the RdRp of FsPV3 is most similar to that of Hulunbuir Parti tick virus 1. In contrast, the CP of FsPV3, as well as the hypothetical protein encoded by ORF3 of dsRNA3, was most similar to cognate proteins encoded by Colletotrichum-associated partitivirus 2. However, the two hypothetical proteins encoded by dsRNA4 showed no significant similarity to the available sequences in the National Center for Biotechnology Information database and encoded no apparent conserved domains. Phylogenetic analysis of the RdRp and CP showed that FsPV3 clustered together with other species in the genus Alphapartitivirus. Given that proteins encoded by FsPV3 are not sufficiently highly homologous to a single known virus and that it encodes two novel proteins, we suggest that FsPV3 should be regarded as a new member of the genus Alphapartitivirus in the family Partitiviridae. This is the first report of FsPV3 infecting F. solani.

Acetylcholinesterase – glucose-regulated protein 78 binding site prediction, a hope to cure neurological disorders such as Alzheimer’s disease

Cerebral amyloid plaques in the brain define the elderly neuralgic disorder, Alzheimer’s disease (AD). The enzyme Acetylcholinesterase (AChE) was reported to play a vital role in AD. It was shown that AChE induces amyloid fibril formation forming highly toxic AChE-Amyloid-β (Aβ) complexes. AChE can accelerate amyloid formation, and its inhibition could prevent such alterations to the enzyme. Understanding the proteostasis of AChE and its binding site to cellular chaperone GRP78 (Glucose-regulated protein 78) would help find a treatment for AD. In this study, the state of the art computational tools were utilized to predict the binding location of AChE that can stably associate with the cellular chaperone, GRP78. Sequence comparison along with molecular docking predicts two binding locations on AChE (C69–C96 and C257–C272) that could bind to GRP78 substrate binding domain β (SBDβ). The analysis of the docking data suggests that the former location has the best average binding affinity value (-12.16 kcal/mol) and average interaction pattern (13.9 ± 3.5 H-bonds, 5.5 ± 1.4 hydrophobic contacts, and 1.4 ± 1.2 salt bridges).

Variability of non-structural proteins of HIV-1 sub-subtype A6 (Retroviridae: Orthoretrovirinae: Lentivirus: Human immunodeficiency virus-1, sub-subtype A6) variants circulating in different regions of the Russian Federation.

HIV-1 non-structural proteins are promising targets for vaccine development and for creating approaches to personalized medicine. HIV-1 sub-subtype A6 has become the dominating strain in Russia. However, the geographic, economic and demographic characteristics of the country can contribute to the formation of differences between A6 variants circulating in different regions. The aim of the study is a comparative analysis of the consensus sequences of non-structural proteins in A6 variants circulating in the Amur Region, in Arkhangelsk, Irkutsk and Murmansk. 48 whole blood samples obtained from HIV-infected patients without experience of therapy observed at the AIDS Centers in Arkhangelsk, Irkutsk, Murmansk and Amur Region were analyzed. HIV-1 whole-genome nucleotide sequences were obtained and were subtyped. Consensus sequences of sub-subtype A6 variants non-structural proteins for each analyzed region were formed. Furthermore, reference sequences of sub-subtype A6 non-structural proteins were formed based on whole-genome sequences retrieved from the international Los Alamos database. Comparison of consensus sequences and references was performed using the MEGA v.10.2.2 and the PSIPRED programs. Vif, Vpr and Nef reference sequences have been obtained for HIV-1 sub-subtype A6. There was not difference in consensus sequences of Vpr in different regions. Characteristic features were found for consensus sequences of Tat, Rev, Vpu, Vif and Nef proteins in different regions. A limitation of the study is a small sample size. Overall, the results demonstrate the existing diversity of non-structural proteins in sub-subtype A6 variants in different regions and indicate the relevance of studying the polymorphism of non-structural proteins of virus variants in different regions.

Bifidobacterium favimelis sp. nov., isolated from black comb honey.

A strain of the bacterial genus Bifidobacterium, IMAU50987T, that was isolated from black comb honey from Lianghe County, Dehong Autonomous Prefecture, Yunnan Province, China, could not be accurately identified as a known species using 16S rRNA gene sequencing. In this study, the taxonomic status of strain IMAU50987T was evaluated using whole-genome sequencing combined with phenotypic analyses. Strain IMAU50987T was Gram-positive, non-motile and non-spore-forming. Comparative of 16S rRNA gene sequence similarity analysis indicated that strain IMAU50987T could be attributed to the genus Bifidobacterium and most closely related to the B. mellis Bin7NT (98.5% identity). Comparative sequence analysis of eight housekeeping genes (pyrG, thrS, glnA1, recA, tuf, dnaB, rpoC and xfp) showed that strain IMAU50987T was different from closely related species. Phylogenomic analysis based on the 88 single-copy genes in the phylogenetic tree showed that strain IMAU50987T belonged to the B. asteroides group. The highest average nucleotide identity value for strain IMAU50987T was 77.0% in comparison with B. choladohabitans B14384H11T and B. apis F753-1T. However, the highest digital DNA-DNA hybridization value was 23.1% compared with B. apis F753-1T and B. xylocopae XV2T; the highest average amino acid identity value was 73.2% compared with B. polysaccharolyticum W8117T. These values are below the accepted threshold for novel species boundaries. The draft genome size of strain IMAU50987T was 1.9 Mb, and the DNA G+C content was 63.5%. The major cellular fatty acids of strain IMAU50987T were C16 : 0, C18 : 1 ω9c and Sum in Feature 7 (C19 : 1 ω7c/C19 : 1 ω6c). The cell-wall peptidoglycan was of the A3α l-Lys-Gly type. Based on data from this study, a novel species, Bifidobacterium favimelis sp. nov., is proposed with the type strain IMAU50987T (= GDMCC 1.4189T = JCM 36315T).

Exploring the mitogenomic of Lottiidae (Patellogastropoda): phylogenetics, gene rearrangement and evolutionary divergence time estimations

BackgroundLottiidae (Gray, 1840) is a derived family of Patellogastropoda and an important component of intertidal benthic communities. The mitochondrial genome (mitogenome) has been frequently used to analyze the phylogenetic relationships of Patellogastropoda. We used next-generation sequencing (NGS) to sequence the complete mitogenomes of five species. We analyzed the basic base composition characteristics of these mitogenomes, constructed a phylogenetic tree, compared the characteristics of gene rearrangement with other related species, and discussed the evolutionary patterns between gastropod species and the evolutionary relationships of each subclass. In addition, we aim to infer the differentiation time and evolutionary characteristics of various species in the order Patellogastropoda. These results will enrich the mitogenome database of Patellogastropoda and enhance our understanding of the genetic characteristics of Lottiidae and the phylogenetic relationships between gastropods.ResultsWe obtained the mitogenomes sequences of Lottia peitaihoensis, Patelloida saccharinoides, Patelloida ryukyuensis, Nipponacmea sp. and Nipponacmea nigrans, using next-generation sequencing technology. We analyzed the basic structural characteristics of their mitogenomes and found that their lengths ranged from 16.6 kbp to 19.1 kbp. While N. nigrans and P. saccharinoides contain 39 genes, L. peitaihoensis, P. ryukyuensis, and Nipponacmea sp. have only 38 genes, with one trnW less. The most abundant base among the five species is T, and most protein coding genes (PCGs) use ATT, ATG, and ATA as starting codons, and TAA and TAG as stopping codons. We selected the mitogenomes of 10 Lottiidae species for selection pressure analysis and found that all PCGs were subject to purifying selection. Phylogenetic analysis indicates that Patellogastropoda is a fundamental branch of the Gastropoda, and Lottiidae, within Patellogastropoda, is an independent branch at the outermost of the entire phylogenetic tree. Comparison of mitochondrial gene sequences of all Patellogastropoda species revealed a high degree of gene rearrangement within the family Lottiidae, eight sequences present among the 10 species examined. By estimating their divergence times, we found that the divergence of limpets occurred as early as the Permian period of the Paleozoic Era, and a large number of species diverged in the Cenozoic Era.ConclusionThe data obtained from this study will provide information on the assembly of the mitochondrial genome of the Lottiidae species, which will contribute to a better understanding of the evolutionary status and relationship among thes family of Patellogastropoda.

Nematode isolation from Creophilus maxillosus (L.) (Staphilinidae) with a description of Rhabditidoides eutrophicola n. sp. (Diplogastridae) and some notes on Diplogastrellus gracilis (Bütschli, 1876) Paramonov, 1952 (Diplogastridae)

Summary Nematodes associated with the carcass beetle Creophilus maxillosus were examined. The beetles were collected from the decomposed body of a dead racoon dog Nyctereutes procyonoides in Kyoto, Japan, and dissected for examination of internal parasites. The dissected beetles were kept on agar plates for isolation of phoretic species. Although no parasites were found, three species of phoretic associates, Caenorhabditis plicata, Diplogastrellus cf. gracilis and Rhabditidoides sp., were recognised, and two species were later successfully cultured as laboratory strains. Diplogastrellus cf. gracilis and Rhabditidoides sp. were compared to an authentic strain of D. gracilis (German strain, SB306) and two presumably conspecific strains (German strain RS5443 and Japanese strain NKZ346), respectively, by mating experiments and molecular sequence comparison. The comparisons revealed that D. cf. gracilis is conspecific to D. gracilis SB306, and three Rhabditidoides strains are new conspecific species. The typological and molecular characters of D. gracilis are described and compared with other populations of the species, and Rhabditidoides sp. is taxonomically described as Rhabditidoides eutrophicola n. sp.

Structure of MltG from Mycobacterium abscessus reveals structural plasticity between composed domains.

MltG, a membrane-bound lytic transglycosylase, has roles in terminating glycan polymerization in peptidoglycan and incorporating glycan chains into the cell wall, making it significant in bacterial cell-wall biosynthesis and remodeling. This study provides the first reported MltG structure from Mycobacterium abscessus (maMltG), a superbug that has high antibiotic resistance. Our structural and biochemical analyses revealed that MltG has a flexible peptidoglycan-binding domain and exists as a monomer in solution. Further, the putative active site of maMltG was disclosed using structural analysis and sequence comparison. Overall, this study contributes to our understanding of the transglycosylation reaction of the MltG family, aiding the design of next-generation antibiotics targeting M. abscessus.

A scallop IκB protein involved in innate immunity acts as a key regulator of NF-κB

Chlamys farreri, a commercially important bivalve mollusk, is extensively cultivated in China. In recent years, the frequent occurrence of diseases has led to significant mortality in scallop farms. Despite this, our understanding of scallop's innate immune mechanisms remains limited. The NF-κB signaling pathway plays a crucial role in various biological processes, including cellular, developmental, and immune defense mechanisms. Inhibitors of NF-κB (IκB) proteins block the nuclear localization and DNA binding of NF-κB, thereby inhibiting its activity. However, the role of these proteins in invertebrates is not well understood. In this study, we identified a new homolog of the IκB gene in C. farreri, named CfIκB1. The open reading frame of CfIκB1 spans 1,089 bp, encoding 362 amino acids. Through sequence comparison and phylogenetic analysis, CfIκB1 was classified as a member of the invertebrate IκB family. Quantitative real-time PCR revealed that CfIκB1 transcripts are present in all examined tissues, with the highest expression observed in hemocytes. Expression levels were significantly upregulated following exposure to lipopolysaccharide, peptidoglycan, and polyinosinic:polycytidylic acid. Co-immunoprecipitation studies confirmed that CfIκB1 interacts with NF-κB family proteins CfRel-1 and CfRel. Dual-luciferase reporter assays demonstrated that CfIκB1 inhibits CfRel-dependent activation of NF-κB, ISRE, IFNβ, and AP-1. These findings suggest that CfIκB1 plays a crucial role in regulating NF-κB activity, which is integral to the innate immunity of C. farreri. This research enhances our understanding of the innate immune system in invertebrates and provides a theoretical basis for developing disease-resistant scallops at the molecular level.

Genome mining approach reveals the CRISPR-Cas systems features and characteristics in Lactobacillus delbrueckii strains

This study employed a comprehensive genome-mining approach to characterize CRISPR-Cas systems in Lactobacillus delbrueckii strains. The analysis involved retrieving 105 genome sequences to explore the variety, occurrence, and evolution of CRISPR-Cas systems within the species. Homology analysis of spacer sequences in detected CRISPR arrays was conducted to assess the variety of target phages and plasmids. The evolutionary trajectories of spaceromes in each subtype of CRISPR arrays were determined by analyzing acquisition and deletion events under the selection pressure of foreign plasmids and phages. Among the analyzed strains, 53 contained only one CRISPR-Cas locus, 11 had two loci, and 21 featured three loci with complete CRISPR-Cas systems. Subtype designation of the results of current study revealed that 56% of these systems belong to subtypes I-E/I-C, 23% to subtypes III-A/III-D, and 17% to subtype II-A. Notably, certain plasmids were found to be specifically targeted by distinct CRISPR array systems. The comparison of spacer sequences with phage genomes indicated that strains containing only CRISPR-Cas type-I systems targeted a broader range of phages. In conclusion, this study highlights the diversity of the three identified CRISPR-Cas types in L. delbrueckii strains and emphasizes their significant role in defense against phage invasion.

Prostaglandin E2-EP2/EP4 signaling induces immunosuppression in human cancer by impairing bioenergetics and ribosome biogenesis in immune cells

While prostaglandin E2 (PGE2) is produced in human tumor microenvironment (TME), its role therein remains poorly understood. Here, we examine this issue by comparative single-cell RNA sequencing of immune cells infiltrating human cancers and syngeneic tumors in female mice. PGE receptors EP4 and EP2 are expressed in lymphocytes and myeloid cells, and their expression is associated with the downregulation of oxidative phosphorylation (OXPHOS) and MYC targets, glycolysis and ribosomal proteins (RPs). Mechanistically, CD8+ T cells express EP4 and EP2 upon TCR activation, and PGE2 blocks IL-2-STAT5 signaling by downregulating Il2ra, which downregulates c-Myc and PGC-1 to decrease OXPHOS, glycolysis, and RPs, impairing migration, expansion, survival, and antitumor activity. Similarly, EP4 and EP2 are induced upon macrophage activation, and PGE2 downregulates c-Myc and OXPHOS in M1-like macrophages. These results suggest that PGE2-EP4/EP2 signaling impairs both adaptive and innate immunity in TME by hampering bioenergetics and ribosome biogenesis of tumor-infiltrating immune cells.

First Isolation and Characterization of Feline Panleukopenia Virus From Wild Raccoon Dogs in the Residential Area of Shanghai, China.

Carnivore parvovirus is commonly detected in canines and felines and results in a range of symptoms, including diarrhoea, with a high lethality rate. In recent years, the gradual restoration of urban ecosystems coupled with a lack of natural predators means that wild raccoon dogs have gradually entered residential neighbourhoods in Shanghai, and the carnivore parvovirus carried by such canines may seriously affect their health and that of dogs and cats in these neighbourhoods. Therefore, it is essential to monitor wild raccoon dogs for carnivore parvovirus. The wild raccoon samples were collected from the residential area of Shanghai and screened for parvovirus, followed by virus isolation and sequence comparison analysis. In this study, three strains of parvovirus, YSH1-2022, YSH2-2022 and GSW1-2023, were isolated from anal and pharyngeal swab mixtures of 42 live raccoon dogs and two dead raccoon dogs in Shanghai, China. After alignment, it was found that the three strains of parvovirus were all located in the same branch as feline panleukopenia virus (FPV), and the three VP2 genes had 100% homology with FPV VP2 genes isolated from Shanghai and Yangzhou, Jiangsu Province. The homology of the three NS1 genes with FPV NS1 isolated from Shanghai and other places was 99.9%-100%. This is the first report of FPV isolated from raccoon dogs. In this study, the host range and risk of infection of parvovirus were evaluated, providing data to support wildlife management and policy formulation in Shanghai.

Genome-wide analyses of Ariadne family genes reveal their involvement in abiotic stress responses in apple

E3 ligases are essential for ubiquitination and play a role in regulating various aspects of eukaryotic life. Ariadne (ARI) proteins, a subfamily of RBR (RING-between-RING) proteins, have been recognized as a new class of RING-finger E3 ligases. Recent research has shed light on their potential involvement in plants’ responses to abiotic stress. However, comprehensive studies on ARI genes in apple (Malus domestica) are still lacking. This study identified ten MdARI genes in the apple genome, and examined intraspecific and interspecific collinearity to explore the evolutionary relationships of ARI family members. Phylogenetic analyses classified MdARIs into two subfamilies (A and B), and by integrating gene structure, conserved motifs, and sequence comparison results, subfamily B was further divided into two subgroups (I and II). Tissue expression analyses revealed varied expression patterns of MdARI genes in different tissues, and subcellular localization showed that MdARI1-1, MdARI1-2, and MdARI9-1 were located in the nucleus, while the other seven MdARIs were distributed throughout the cell. Analyses of promoter cis-elements and expression patterns under cold, salt, and drought treatments indicated the involvement of MdARIs in abiotic stress responses. Several proteins crucial to the plant stress response were predicted to be potential MdARIs-interacting proteins based on the protein interaction network. Additionally, the interaction between UBC11 (E2) and MdARI7-2 was confirmed by a yeast two-hybrid (Y2H) experiment, suggesting that MdARI7-2 may function as an E3. These findings will greatly benefit future research on the role and mechanisms of ARI proteins in apple stress response.

Metagenomic Detection of Multiple Viruses in Monk Parakeet (Myiopsitta monachus) in Australia.

Birds are known to harbour many pathogens, including circovirus, herpesviruses, adenoviruses and Chlamydia psittaci. Some of these pose zoonotic risks, while others, such as beak and feather disease virus (BFDV), have a significant impact on the conservation of endangered bird species. This study was aimed to determine the faecal virome of a group of apparently healthy Monk parakeet using high-throughput sequencing. Fresh faecal samples were collected from four Monk parakeets at a pet shop in Melbourne, Australia. Virus enrichment and nucleic acid extraction were performed on the faecal samples, followed by high-throughput sequencing at the Australian Genome Research Facility (AGRF). Utilising an established pipeline for high-throughput sequencing data analysis, this study revealed the presence of three viruses of the families Circoviridae, Parvoviridae and Adenoviridae. Subsequent sequence comparison and phylogenetic analyses further confirmed that the detected viruses belong to the genera Chaphamaparvovirus (unassigned species), Circovirus (species Circovirus parrot) and Siadenovirus (species Siadenovirus viridis). Despite non-pathogenicity, the existence of multiple viruses within a bird species underscores the risk of these viruses spreading into the pet trade. Detection and a better understanding of avian viruses are crucial for the establishment of appropriate management and biosecurity measures in the domestic and international bird trade, which ultimately supports the conservation of vulnerable bird species.