MEGA6: Molecular Evolutionary Genetics Analysis version 6.0

Combining whole genome and transcriptome sequencing to analyze the pathogenic mechanism of Diplodia sapinea blight in Pinus sylvestris var. mongolica Litv

Diplodia sapinea (= Sphaeropsis sapinea) is an opportunistic pathogen that usually lives in symbiosis (the coexistence of dissimilar organisms) with its host and can cause disease under extreme climatic or physiological stress. In this study, we generated a high-quality genome map of D. sapinea using PacBio Circular Consensus Sequencing (CCS) technology and analysed the key disease-causing genes of D. sapinea by RNA sequencing (RNA-seq). In the study, a number of cell wall degrading enzyme genes were identified to be up-regulated during pathogen infection, which may be involved in biotic stress response in P. sylvestris var. mongolica Litv. It was also found that the expression of antioxidant-related genes, such as those involved in carotenoid biosynthesis, ascorbate and glutathione metabolism, was up-regulated in the P. s. var. mongolica Litv. after fungus infection. Differently expressed genes (DEGs) -based protein-protein interaction (PPI) network was constructed that included 163 pairs of significantly positively correlated proteins, forming three highly interacting gene clusters, and the PPI network was predicted to be associated with the replication and propagation processes of the fungus. These results provide important information for understanding the pathogenic mechanisms of Diplodia tip blight and developing control strategies in P. s. var. mongolica Litv.

Environmental bovine subclinical mastitis gram-negative pathogens: Prevalence, antimicrobial resistance with special reference to extended-spectrum β-lactamases and carbapenemase production

This study investigates mastitis in the dairy industry, with a focus on the issue of antibiotic resistance. This study was designed to evaluate mastitis prevalence and investigate the bacteriological profiles of subclinical mastitis (SCM) milk, mastitis-free milk, and market milk. Out of 374 quarter milk samples, 26.2 % were from animals with SCM. Bacteriological examination identified 87 Gram-negative bacterial strains from subclinical mastitis milk (SCMM) (42.9 %), subclinical mastitis-free milk (SCMFM) (17.97 %), and market milk (MM) (58 %). MALDI-TOF MS identified species including E. coli, K. pneumoniae, Enterobacter cloacae, Citrobacter freundii, Serratia marcescens, and Acinetobacter baumannii, with E. coli being the most frequent. Multi-drug resistant (MDR) phenotype was found in 43.7 % of isolates, with 57.1 % from SCMM, 43.8 % from SCMFM, and 24.1 % from MM. Biofilm production was observed in 44.8 % of isolates, with a significant correlation between MDR and biofilm formation. Eight strains (9.2 %) were extended-spectrum β-lactamases (ESBLs) producers, with blaCTX-M, blaTEM, and blaSHV genes detected. A. baumannii harbored multiple resistance genes, including blaTEM, blaCTX-M, blaOXA51, blaOXA23, and blaNDM, showing both phenotypic and genotypic ESBLs and carbapenemase activity. The presence of MDR, ESBLs, and carbapenemase producing Gram-negative bacteria in SCMM, SCMFM, and MM indicates a concerning exchange of bacteria and antimicrobial resistance genes between human and animal hosts, posing risks of milk contamination and environmental hazards. A one-health approach is essential for controlling antimicrobial-resistant bacteria, emphasizing prudent antimicrobial use in human and animal healthcare, and improving farm hygiene practices.

Molecular phylogeny by Bayesian analysis and description of a new species of Henneguya, a parasitic cnidarian from Astyanax bimaculatus (Linnaeus, 1758) (Characiformes: Acestrorhamphidae) in Caatinga: A biome with neglected biodiversity data

Myxozoans are cnidarian parasites with a worldwide distribution and represent some of the most spectacular examples of parasite radiation. Based on an integrative taxonomic approach that includes spore morphology and molecular data, as well as other phenotypic characters such as host specificity, a new myxozoan, Henneguya caraubensis n. sp., is described from the gills of Astyanax bimaculatus (Linnaeus, 1758). Plasmodia were located within the gill lamellar epithelium, without connective tissue surrounding them. Mature myxospores were ellipsoidal in the frontal view, measuring 27.2 ± 2.6 μm in total length, 10.3 ± 0.7 μm in body length of spore, and 3.9 ± 0.2 μm in width. Two polar capsules elongated pyriform in shape, equal in size, measuring 3.4 ± 0.3 μm in length and 1.2 ± 0.1 μm in width. Polar tubules had 5 to 6 coils. Histopathological analysis showed large intralamellar polysporic plasmodia associated with displacement, deformation, and fusion of the nearest gill lamellae and with the adjacent lamellae being pushed laterally. Bayesian inference SSU rDNA-based phylogenetic analyses showed a strong tendency of Henneguya/Myxobolus species to form clusters mainly based on the order and/or family of the host, despite having different geographic origins. Phylogenetically, the novel species grouped within a clade containing Henneguya/Myxobolus spp. and appears in a well-supported subclade of Henneguya species parasites of Astyanax fishes. Our study reinforces highly endemic diversity still hidden that inhabits the Caatinga biome and points out the need to improve the strategies of protection and conservation of this threatened ecoregion with neglected biodiversity data.

The vacuole pH-related gene RcNHX2 affects flower color shift and Na+ homeostasis in roses

Rose (Rosa spp.) is one of the most famous ornamental plants in the world, and its commodity value largely depends on its flower color. The color of roses mainly depends on the composition and state of anthocyanins, and the vacuolar pH value is an important factor affecting the stability and state of anthocyanins. The vacuolar sodium/proton antiporters (NHXs) play important roles in the maintenance of cellular ion homeostasis and petal vacuolar pH. However, the NHX functions related to rose flower coloration remain relatively uncharacterized. In this study, we cloned and characterized the vacuolar pH-related gene RcNHX2, which encoded a vesicular cation/H+ antiporter protein. Phylogenetic sequence analysis revealed that RcNHX2 belongs to the vesicular NHX family of proteins. It is localized in the vesicular membrane, where it exerts its function. RcNHX2 was significantly differentially expressed in different color-presenting types of petals of roses, and it was particularly highly expressed in the blue-purple petals. The overexpression of RcNHX2 in Rosa hybrida 'Florentina' caused the pH to increase and the petal color to change from red to blue-purple. On the basis of virus-induced gene silencing, we determined that decreased RcNHX2 expression significantly reduces R. hybrida 'Blue For You' petal coloration. We indicated that RcNHX2 might be involved in the color shift to blue in roses. Moreover, it was observed that in the cells of the rose plants in which RcNHX2 was silenced, the Na+ homeostasis was affected. The results suggest that the vesicular Na+/H+ transporter, RcNHX2 gene, likely plays a crucial role in the blue color change and the maintenance of cellular Na+ homeostasis in roses. These findings offer valuable insights for the cultivation of blue rose.

Pathogenicity of a chicken-origin cluster 3 isolate of Tembusu virus in Pekin ducklings and Kunming mice

Tembusu virus (TMUV) is genetically classified into three clusters. To date, information relating to the pathogenicity of TMUV cluster 3 in ducks is limited; whether TMUV cluster 3 has the potential to induce disease in mice remains unclear. Here, we evaluated the pathogenicity of a chicken-origin TMUV cluster 3 strain G (TMUV/G) in 5-day-old Pekin duck and 3-week-old Kunming mouse models by comparing with TMUV cluster 2.1 strain H (TMUV/H). TMUV/G caused neurological diseases in both ducklings and mice. Whereas TMUV/G was less virulent than TMUV/H, with more mild clinical signs and microscopic lesions and significantly lower morbidity. TMUV/G caused 10 % mortality in ducklings and failed to cause mortality in mice, in sharp contrast with 90 % mortality in ducklings and 60 % mortality in mice induced by TMUV/H. Further analysis with the mouse model revealed that TMUV/G replicated to lower levels in the central nervous system, and induced lower IFN-β, IL-6, TNF-α, and Viperin responses in the infected cerebrum. Compared with TMUV/H, TMUV/G contained a number of mutations throughout the genome and had a reduced replication efficiency in cultured hippocampal neuronal (HT22) cells. Together these findings suggest that TMUV/G displays markedly lower virulence in Pekin ducklings and Kunming mice relative to TMUV/H, indicating that different virus-host interactions exist between cluster 3 and 2.1 TMUVs. The present work contributes to the understanding of virulence phenotype of TMUV cluster 3, and will stimulate further studies on the mechanism for substantial virulence attenuation of TMUV cluster 3 relative to TMUV cluster 2.1.

Identification and characterization of PcHD8 from Pogostemon cablin related to the regulation of trichome development

Pogostemon cablin, a herbaceous plant of the Lamiaceae family, is widely recognized for the medicinal and industrial applications of its dried aerial parts. The plant's surface is densely populated with trichomes, which are believed to be the primary sites for the biosynthesis and accumulation of patchouli essential oil. However, the molecular mechanisms underlying the development of these trichomes in P. cablin remain largely unexplored. This study employed transcriptomic sequencing to identify and characterize genes co-regulated in trichome development and essential oil biosynthesis in P. cablin. Notably, we report the first identification of PcHD8, a member of the HD-ZIP gene family. Homologous genes, such as AaHD8 in Artemisia annua and SlHD8 in Solanum lycopersicum, have been shown to promote both trichome formation and secondary metabolite synthesis. We cloned PcHD8 and overexpressed it in Nicotiana tabacum, which resulted in a significant increase in trichome density compared to the control. Conversely, silencing PcHD8 via virus-induced gene silencing (VIGS) in P. cablin led to a marked reduction in trichome density. GC-MS analysis revealed a significant decline in the key biomarkers of patchouli essential oil, patchouli alcohol and pogostone, following PcHD8 silencing. These findings establish PcHD8 as a key positive regulator of trichome development and essential oil biosynthesis. This study offers critical insights into the genetic regulation of plant traits affecting medicinal quality. Our findings highlight PcHD8 as a promising candidate gene for molecular breeding in P. cablin and may provide a reference for research on other trichome-rich, volatile oil-producing plants.

A novel F-box gene, SlSE2.2, is responsible for the stigma exsertion degree in tomato (Solanum lycopersicum)

Tomato stigma exsertion is an important trait in positional sterility genotypes, which can eliminate the need for manual emasculation and promote hybrid production. In this study, we discovered a new tomato accession, J59, with a stably inherited stigma exsertion trait. To explore the regulatory genes of the stigma exsertion trait, J59 and inserted stigma genotypes M82 were crossed to obtain mapping populations. Through three years mapping, a quantitative trait locus (QTL) associated with the stigma exsertion trait was narrowed down to a 52.635 kb interval on chromosome 2, Solyc02g087270 was identified as the candidate gene responsible for this trait, named SlSE2.2. This gene encoded an F-box protein of the FBA subfamily. Sequences analysis revealed that an 11 bp deletion occurred in the first exon of SlSE2.2 in J59, resulting in premature termination of translation. Subcellular localization revealed that SlSE2.2 is located to the nucleus. Knockout of SlSE2.2 increased anther and style lengths, which reduced the values of anther length minus pistil length, changing the relative length of anthers and pistils, called stigma exsertion degree, whereas, overexpression of SlSE2.2 showed the opposite phenotype. Hormone levels analysis revealed that SlSE2.2 negatively modulated IAA, ETH, and JA levels and positively modulated ABA content. Transcriptomic analysis showed that SlSE2.2 affected the expression of SlIAA19, SlIAA36, SlETR6, SlJAZ, and SlSnRK2 related to the hormone signal transduction. This study identified the important role of a new gene, SlSE2.2, which provided a helpful insight to explore the regulatory mechanisms of stigma exsertion degree in tomato.

Novel anti-herpes simplex activity of Chryseobacterium indologenes: Genomic and metabolomic insights

Herpes simplex virus (HSV) is a pathogenic virus responsible for various diseases, necessitating alternative antiviral strategies for HSV-1 treatment. Given the antiviral properties of lactic acid (LA), we screened rhizobacteria from the maize (Zea mays L.) rhizosphere for organic acid production. Among the isolates, SR50, SR126, and SR135 exhibited significant LA production, confirmed by High-Performance Liquid Chromatography (HPLC) analysis. Their antiviral efficacy against HSV-1 was evaluated by determining IC50 values and selectivity indices (SI = CC50/IC50), with SR50, SR126, and SR135 displaying SI values of 135.14, 10.74, and 2.17, respectively. SR50, identified via 16S rRNA sequencing as Chryseobacterium indologenes, was selected for further antiviral analysis. The cell-free supernatant (CFS) of SR50 demonstrated 73.3 % inhibition of viral adsorption, 60 % virucidal activity, and a 46.7 % reduction in viral replication. Metabolomic profiling using Gas Chromatography-Mass Spectrometry (GC-MS) identified short- and long-chain organic fatty acids. Whole Genome Sequencing (WGS) revealed a 4,581,372 bp genome encoding diverse biosynthetic pathways, including siderophores, plant hormones, terpenoids, polyketides, and other bacterial secondary metabolites. Additionally, genes encoding lactaldehyde dehydrogenase and pyruvate dehydrogenase confirmed the presence of lactic and acetic acid biosynthesis pathways. This study presents the first report of C. indologenes SR50 exhibiting anti-HSV-1 activity, highlighting its potential as a novel antiviral resource.

Genetic mixed diversity landscape in the paternal lineages of 11 populations inhabiting Southwest China according to the analysis of 25 Y-STRs

Y-STR genotyping can be used to predict the genetic mixed landscape of different populations effectively. In this study, 25 Y-STR loci were detected in 745 unrelated healthy males from the Bai, Bouyei, Dong, Gelao, Hui, Maonan, Mulao, Shui, Tujia, Yi and Han groups in Guizhou Province via a Y27Plex fluorescence detection kit. The results revealed that the kit had high gene diversity (GD: 0.0878 ~ 0.9581; HD: 0.9781 ~ 0.9987). The genetic distance ranged from 0.0172-0.3750. On the basis of PCA, phylogenetic tree and structure analysis, the same language groups tended to show closer genetic relationships among the 11 sample populations. According to the genetic relationship analysis of the 11 samples and 22 reference populations, the genetic relationships of Guizhou Han and Guangxi Gin were the closest (0.018), whereas those of the Tujia and She nationalities were the farthest in Guizhou (0.4483). Additionally, Guizhou Tujia, Guizhou Hui, Xinjiang Mongolians, Yunnan Lahu, Kazakh Uzbekistan and Kazakhstan were clustered together. This study provides a reference for the genetic structure and genetic differentiation of 11 indigenous populations in Guizhou Province and provides useful paternal information for population genetics, archaeology and historical research.

Two new acremonium-like species, Paragibellulopsissinensis sp. nov. and Phialoparvumsinense sp. nov. (Sordariomycetes, Ascomycota) from China

Paragibellulopsis and Phialoparvum, both erected in 2018, currently comprise merely one and three validly published species, respectively. The identification of two new species, Paragibellulopsissinensis and Phialoparvumsinense, was achieved by analyzing morphological characteristics and phylogenetic data obtained from four molecular markers (ITS, LSU, rpb2, and tef-1α). Morphologically, Pa.sinensis possessed short conidiogenous cells and aseptate and smaller conidia. On the other hand, Ph.sinense had obovate conidia and longer phialides. Phylogenetic analysis revealed that Pa.sinensis formed an independent branch as a sister species to Pa.chrysanthemi, whereas Ph.sinense clustered in a monophyletic clade with a stable topology. The maximum likelihood bootstrap ratio and the Bayesian inference posterior probability provided robust statistical evidence, indicating the presence of two novel species within the genera of Paragibellulopsis and Phialoparvum. The present study contributes to the discovery of species diversity in Paragibellulopsis and Phialoparvum.

Enhanced Resistance to Pokkah Boeng Disease in Sugarcane Through Host-Induced Gene Silencing Targeting FsCYP51 in Fusarium sacchari

Pokkah boeng disease (PBD), a common and highly destructive disease of sugarcane, is mainly caused by Fusarium sacchari. Breeding sugarcane resistant to PBD is challenging due to the limited availability of immune or highly resistant germplasm resources. Host-induced gene silencing (HIGS) based on RNA interference (RNAi) is a promising disease-control method that offers strong disease-targeting ability with low environmental impact. This study found that silencing either three FsCYP51 genes (FsCYP51A, FsCYP51B and FsCYP51C) simultaneous or two of them (FsCYP51A and FsCYP51C) could inhibit the growth, development, and virulence of F. sacchari. Subsequently, we developed CYP51-HIGS transgenic sugarcane lines using gene-gun genetic transformation and obtained seven lines expressing dsFsCYP51. Both the results of laboratory inoculation assays and field trials indicated that all the seven transgenic lines had significant resistance to PBD. Moreover, in the field trials, the yield losses of transgenic sugarcane due to PBD were reduced compared with those of the control. This is the first report using the HIGS strategy to inhibit PBD infection in sugarcane. This breakthrough provides clear guidelines and practical approaches for the future breeding of sugarcane varieties with strong antifungal resistance.

Ability to use ITS and rbcL sequencing for determination of the genetic diversity and relationships among olive (Olea europaea L.) genotypes

Olives are of considerable economic and commercial importance and are mostly used in both daily life and industries. The DNA barcode method has a lot of potential for reviving the science of arithmetics and traditional biodiversity studies, so it has been widely used on plants and for classification and arithmetic purposes. In this study, we sequenced seven different olive genotypes (Olea europaea cv. Olive yellow, O. europaea cv. Oliy, O. europaea cv. Roodbar Oily, O. europaea cv. Mari, O. europaea cv. Fishemi, O. europaea cv. Manzanila, O. europaea cv. Koroneiki) to study their diversity and evolution. The data were analyzed using Clustalw2 and BioEdit software. The homology rate of rbcL and ITS sequences was all in the range of 97-100%. It was identified, for ITS, 1,059 genetic luci (580 luci without deletion and addition and 479 luci with deletion and addition (328 luci polymorphs, 151 monomorphs), 217 singletons, and for rbcL, 565 genetic luci with ( 60 luci without deletion and addition and 505 luci with deletion and addition (2 luci with polymorphs, 503 monomorphs), 1 singleton. It was determined that the number of four haplotypes (haplotype diversity index = 0.80) was determined for ITS and three haplotypes (haplotype diversity index = 0.71) for RBCL. The results indicated that in the nucleotide sequence of the ITS gene among olive varieties, guanine was the most abundant base at 28.7%, while adenine had the lowest abundance at 5%. In contrast, the rbcL gene showed that thymine was the most abundant base at 29.8%, with cytosine being the least abundant at 20.6%. Estimates of nucleotide transitions in the ITS gene revealed a high frequency of pyrimidine transitions, with a thymine-to-cytosine transition rate of 16.84% and a cytosine-to-thymine transition rate of 11.63%. The ITS primer successfully identified and separated only six genotypes, whereas rbcL identified all seven genotypes. Although the success rates of 60-70% for both ITS and rbcL may not seem particularly high, they still significantly contribute to large-scale biodiversity inventories, especially for olive species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04336-z.

Molecular mechanism of SmMYB53 activates the expression of SmCYP71D375, thereby modulating tanshinone accumulation in Salvia miltiorrhiza

Tanshinones are bioactive diterpenoid chemicals of the herb Salvia miltiorrhiza with a characteristic furan D-ring. As a newly identified downstream enzyme, SmCYP71D375, catalyzes hydroxylation by 14,16-ether (hetero)cyclization to form the furan D-ring from the precursor of the phenolic abietane-type diterpenoids that exist widely in Lamiaceae plants. However, its transcriptional regulatory network, with SmCYP71D375 as the direct target gene, remains unclear. In the present study, the promoter of SmCYP71D375 was employed as the bait to mine the upstream regulatory protein using the cDNA yeast library of S. miltiorrhiza. An R2R3-MYB transcription factor gene, SmMYB53, was identified. Overexpressing SmMYB53 in transgenic hairy roots upregulated SmCYP71D375 expression, thereby accelerating tanshinone accumulation, whereas tanshinone accumulation was inhibited in SmMYB53-RNAi transgenic hairy root lines. To dissect the regulatory network of SmMYB53, SmbZIP51 was captured using SmMYB53 as the bait to prey for its potential interacting proteins in the cDNA yeast library. Yeast two-hybrid, glutathione S-transferase pull-down, and bimolecular fluorescence complementation assays were independently used to verify the interaction between the SmMYB53 and SmbZIP51 proteins . We further verified that the upregulation of SmCYP71D375 activated by SmMYB53 would be inhibited by the interaction of SmMYB53 and SmbZIP51. The present findings uncover the molecular regulatory network underlying SmCYP71D375 as the direct target regulating tanshinone biosynthesis and offer a basis for the genetic improvement of medicinal substance biosynthesis in S. miltiorrhiza.

Prevalence and molecular characterization of Acute hepatopancreatic necrosis disease (AHPND) in cultured white-leg shrimp Litopenaeus vannamei with the fungal bioactive control strategy

Mass mortalities with clinical signs characteristic of acute hepatopancreatic necrosis disease (AHPND) were reported in cultured Litopenaeus vannamei from three Egyptian farms: Wadi-Mariote, Berket Ghalyoun, and Qarun Lake. During 4-month surveillance in 2023, shrimp samples were collected to investigate the prevalence of AHPND-causing Vibrio parahaemolyticus (VpAHPND) based upon phenotypic identification, PCR, and DNA sequencing of pirA genes and pirB toxin genes followed by maximum likelihood phylogenetic analysis. In addition, the pathogenicity of V. parahaemolyticus was evaluated through the injection challenge and histopathological examination. Moreover, the antibacterial activity of marine fungal extracts against identified V. parahaemolyticus was also assessed. Molecular analysis confirmed both pirA (282 bp) and pirB (392 bp) toxin genes in the bacterial isolates. A significant positive correlation (P < 0.05) was found between V. parahaemolyticus levels in shrimp and pond water samples throughout the study period. Injection challenge with 2.7 × 104 CFU bacterial suspension resulted in 63.33 % mortality in challenged shrimp, with typical AHPND clinical signs. The histopathological examination revealed degenerative changes, including atrophy, necrosis, and sloughing of hepatopancreatic tubule epithelial cells, along with loss of functional hepatopancreatic cells. Among 11 fungal isolates screened for anti-vibrio activity, Aspergillus niger HMA9 showed the strongest inhibitory effect against V. parahaemolyticus. This study provides the first genetic confirmation of pirA and pirB toxin genes in VpAHPND as the cause of L. vannamei mass mortalities in Egypt. Further, it demonstrates the potential of fungal bioactive compounds for controlling AHPND in shrimp aquaculture.

Function of two newly identified Spätzle genes in innate immune response of Macrobrachium nipponense against WSSV infection

Spätzle (Spz) is an extracellular ligand of the Toll receptor and is involved in the innate immunity of crustaceans. Two Spz genes from the oriental river prawn Macrobrachium nipponense (named MnSpz4 and MnSpz5) were found in this study to study the diversity of Spz. These two Spzs all have a Spätzle domain. MnSpz4 and MnSpz5 are closely related in the phylogenetic tree and are grouped into one cluster. However, MnSpz4 and MnSpz5 are distant from the four previously reported Spzs in the phylogenetic tree and belong to another cluster. Quantitative reverse transcription PCR analysis showed that MnSpz4 and MnSpz5 were expressed in all tested tissues of M. nipponense and the highest expression levels of MnSpz4 and MnSpz5 were in the hepatopancreas. After stimulation by the white spot syndrome virus (WSSV), MnSpz4 and MnSpz5 were upregulated to varying degrees at different times. The result of RNA interference showed that the knockdown of MnSpz4 or MnSpz5 downregulated the expression levels of seven antimicrobial peptide (AMP) genes in the stomach of M. nipponense. After the knockdown of MnSpz4 or MnSpz5, the expression of viral envelope protein VP28 showed a significant upregulation. Our results suggested that MnSpz4 and MnSpz5 are involved in innate immunity during WSSV infection and play a negative role in WSSV replication in M. nipponense.

Gastrointestinal parasites and molecular characterization of Eimeria spp. among imported small ruminants in the Sultanate of Oman

The Omani market imports live sheep and goats from across the globe to meet the high human demand for fresh meat. However, this reliance on imports may increase the risk of introducing foreign pathogens despite the strict quarantine regulations. Therefore, we aimed to determine endoparasites among imported sheep and goats that may escape through the sole quarantine station in Muscat. For this purpose, 205 sheep and 47 goats' fecal samples were collected from animals imported from different countries at the Central Quarantine Station in Muscat between 2019 and 2020. The identification and quantification of parasites were revealed by parasitological and molecular techniques, and sequencing analyses were performed on the highly prevalent parasites. The fecal flotation test showed an overall prevalence of gastrointestinal parasites in sheep and goats at 73.17 % and 78.72 %, respectively. The most abundant enteric parasites were Eimeria spp. (65.08 %), strongyle nematodes (25.7 %), and mixed infections of both (19.1 %). In contrast, Strongyloides spp. (2.78 %), Trichuris spp. (2.38 %), and Moniezia spp. (0.40 %) were present to a lesser extent. The McMaster technique revealed an average of 15,325 oocysts and 646 eggs per gram of feces for Eimeria spp. and strongyle-type eggs, respectively. The sequence analyses of the infected sheep and goats showed high similarity with sequences of Trichostrongylus spp., Oesophagostomum columbianum, Haemonchus contortus, and Eimeria spp. Rigorous control measures are essential at Omani quarantine stations to inhibit the entry of new parasites into the country and to mitigate the dissemination of various cross-border gastrointestinal parasites. This may pose a significant risk to public health and livestock productivity.

Morphological and molecular characterization of a new microsporidium, Neoflabelliforma leuchtenbergianum n. sp. from the adipose tissue of Diaphanosoma leuchtenbergianum (Crustacea: Sididae) in China

This study describes a new microsporidian species from the adipose tissue of Diaphanosoma leuchtenbergianum collected from a eutrophic water body of Lianyungang city, Jiangsu province, China. Infected cladocerans exhibited opacity due to the accumulation of numerous spores in the adipose tissue. The earliest stages observed were uninucleate meronts which were in direct contact with the host cell cytoplasm. Multinucleate sporogonial plasmodia underwent plasmotomy to form uninucleate sporoblasts. Mature spores were ovoid, monokaryotic, and measured 4.80 ± 0.37 (4.09-5.23) µm in length and 2.64 ± 0.15 (2.34-3.01) µm in width. The polaroplast was bipartite with the tightly packed anterior lamellae and posterior tubules. The isofilar polar filament coiled in 9-10 turns and arranged in 2-3 rows. The exospore was covered with tubular projections and consisted of four layers. Phylogenetic analysis based on the SSU rDNA sequence indicated that the present species clustered with two Neoflabelliforma species (N. dubium from freshwater oligochaetes and N. aurantiae from freshwater daphnia) and an unidentified microsporidium from soil with high support values to form a solitary branch in microsporidia. Based on the morphological characteristics, ultrastructural features, and SSU rDNA-inferred phylogeny, a new species was named as Neoflabelliforma leuchtenbergianum n. sp.

Identification and breeding exploitation of dBrGMSP related to early bolting in Brassica rapa

Bolting is an important agronomic trait for stalk type of vegetable crops. Early bolting is a favorable characteristic for stalk type of Chinese cabbage variety, which has the advantage of early market supply. In the present study, we screened an EMS-mutagenized Chinese cabbage population and isolated a dominant gain-of-function early bolting mutant ebm16 which exhibited remarkable earlier bolting trait than its WT. BrGMSP, encoding a galactose mutarotase-like superfamily protein, was identified as the candidate gene via MutMap and KASP analysis. A C-T mutation existed in exon of BrGMSP in ebm16. Both transient overexpression in the WT and stable transgenic overexpression in Arabidopsis thaliana for the mutated gene dBrGMSP verified the function of BrGMSP in regulating early bolting. BrGMSP was localized in the nucleus. LCA proved that BrGMSP could interact with BrPGM1 controlling photosynthetic carbon flow. VIGS verified that BrPGM1 had the function on promoting bolting in Chinese cabbage. It was proved that dBrGMSP could be applied in breeding for stalk type of Chinese cabbage.

PacBio-based de novo transcriptomics of the coconut rhinoceros beetle Oryctes rhinoceros identifies physiologically important full-length genes and sheds insights into the molecular relationship (chitin synthase) between Scarabaeidae (Coleoptera) and Hymenoptera

The sparser molecular data in non-model insects such as Oryctes rhinoceros prompted us to investigate and identify its physiologically important genes using the novel PacBio Iso-Seq Sequel II platform with single-molecule real-time (SMRT) technology. SMRT library was prepared from various tissues and sequenced. In total, 16,916,297 subreads clustered into 17,547 contigs which collapsed to form 8708 full-length sequences out of which 4352 functionally annotated transcripts were identified. Genes involved in innate immunity, growth and development, hormonal regulation, cellular process, peritrophic membrane, melanogenesis, integument, circulation, cuticle formation, glycan metabolism, etc., were identified. The transcripts' orthologues were identified predominantly in Coleoptera and Hymenoptera in which chitin synthase (CHS), toll, haemocytin, serine protease/limulus clotting factor c, vitellogenin and trehalose transporter exhibited significant molecular relationships between these two insect orders. Chitin synthase 8 (CHS-8) found in ant has been identified for the first time in the order Coleoptera. (O. rhinoceros) at the translational level and projected a potential to explore evolution (horizontal gene transfer) of CHS in insects. The findings will bridge the molecular data between the genome and transcriptome of O. rhinoceros, thus helping develop molecular targets for its control and management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04348-9.

Characteristics and virulence gene profiles of a pathogenic Lactococcus garvieae isolated from diseased Macrobrachium rosenbergii

Macrobrachium rosenbergii is a commercially important freshwater prawn cultured on a large scale mostly in south and south east Asian countries. Diseases are one of the bottlenecks for the successful culture and production of this important species. Lactococcus garvieae is a Gram-positive coccus commonly found in aquatic environments causing fish and shellfish diseases. In the present investigation, we have isolated and characterized L. garvieae, as etiological agent of white muscle disease in freshwater prawn juveniles. The infected prawn samples showing clinical signs of opaque and whitish muscles, sluggishness and mortality were collected and processed. The isolated bacterium was identified using biochemical methods and 16s rDNA sequencing and species-specific PCR. The sequence obtained revealed > 99% identity with L. garvieae reported elsewhere. Koch's postulate was experimentally established through intramuscular challenge and the infected prawn muscle revealed massive coagulative necrosis with the presence of cocci. The isolate was found to be resistant to antibiotics namely clindamycin, cefoxitin, amoxicillin and co-trimoxazole. The heavy metal tolerance assay revealed the isolate to be tolerant to Cu2+ and Cr6+ and less tolerant to Hg2+. Class I integron was also identified in L. garvieae isolate. Further, the isolate was screened for several virulence genes and found to have hemolysins 1, 2, and 3, adhesin PsaA, adhesin Pav, enolase, LPxTG 1, 3, and 4, adhesin clusters 1 and 2, and adhesin in the PCR assay. It is the first report of L. garvieae infection in freshwater prawns in India and will pave the way for developing suitable preventive measures for future sustainable culture and production of this important aquaculture species.

Biochemical characterization of benzaldehyde dehydrogenases from petunia

Benzoic acid, the simplest aromatic carboxylic acid, is an important building block for a wide range of primary and specialized plant metabolites. In Petunia hybrida, benzoic acid serves as a key precursor of volatile benzenoids, which are responsible for the primary floral scent. However, the enzymes responsible for benzoic acid production in plants have rarely been reported. This study aimed to identify and characterize benzaldehyde dehydrogenases-enzymes that catalyze the oxidation of benzaldehyde to benzoic acid-using a combination of metabolite analysis and transcriptomic approaches. We identified two petunia benzaldehyde dehydrogenases, PhBALDH-1 and PhBALDH-2, with apparent Km values of 93 and 51 μM for benzaldehyde, respectively. While PhBALDH-2 exhibited a strong preference for NAD+ as a cofactor, PhBALDH-1 was capable of utilizing both NAD+ and NADP+. In vitro mutagenesis experiments demonstrated that substituting a single amino acid markedly affected the cofactor specificity of the PhBALDH-1 enzyme. Gene expression analysis during petunia flower development suggests that both PhBALDH-1 and PhBALDH-2 are likely involved in regulating volatile benzenoid biosynthesis in petunia flowers. Our findings provide functional insights into the biosynthesis of benzoic acid and its regulation in P. hybrida.

Decoding the chloroplast genomes of five Iranian Salvia species: insights into genomic structure, phylogenetic relationships, and molecular marker development

BACKGROUND

The genus Salvia, a prominent member of the Lamiaceae family, is renowned for its ecological, medicinal, and economic significance. Despite its importance, molecular data, particularly chloroplast (cp.) genome information, remain scarce for many native Iranian Salvia species. In this study, we sequenced and analyzed the complete cp. genomes of five Iranian Salvia species (S. aethiopis, S. sclarea, S. glutinosa, S. verticillata, and S. officinalis) to elucidate their genomic structure, evolutionary relationships, and potential for biotechnological applications.

RESULTS

The cp. genomes of the five Salvia species exhibited a conserved quadripartite structure, with sizes ranging from 151,163 to 151,662 bp, and a GC content of 38%. Each genome contained 132 or 131 genes, comprising 86 or 87 protein-coding, 8 rRNA, and 37 tRNA genes, with duplications in rpl2, rpl23, and rps12. Minor variations in gene content were observed, such as the absence of trnS-CGA in S. glutinosa. Comparative analysis of IR boundaries showed subtle expansions in S. officinalis and S. sclarea, while S. glutinosa remained stable. Trans-splicing of the rps12 gene was observed in all species, with complex structures in S. glutinosa and S. sclarea. Codon usage analysis revealed a preference for A/U-ending codons, with S. verticillata displaying unique patterns. Nucleotide diversity (Pi) identified highly variable regions, such as rpl14-rpl16 and psbK-psbI, as potential molecular markers. Phylogenetic analysis resolved distinct clades, with S. aethiopis and S. sclarea forming a close group, S. glutinosa clustering with S. chanryoenica, and S. officinalis showing genetic homogeneity with Mediterranean species. S. verticillata exhibited an earlier divergence, highlighting the genus's evolutionary complexity.

CONCLUSIONS

This study provides critical genomic resources for species identification, phylogenetic studies, and the development of molecular markers, facilitating the conservation of native Salvia species and their utilization in breeding programs for medicinal and aromatic traits.

Phylogenetic analysis and pyrethroid resistance mutation profiling of Haematopinus tuberculatus in buffaloes from Naqadeh, Iran

Haematopinus tuberculatus is a major ectoparasite of water buffaloes, causing substantial economic losses. Widespread pyrethroid use has driven the emergence of resistance in H. tuberculatus populations, highlighting the need for a deeper understanding of the underlying genetic mechanisms. This study examined the genetic diversity and resistance mechanisms of H. tuberculatus from Naqadeh, Iran, analyzing 372 lice samples collected from 71 buffaloes across 10 farms. Molecular identification, based on mitochondrial cox1 partial sequence amplification and sequencing, confirmed all samples as H. tuberculatus and revealed close genetic relatedness to populations from China. Phylogenetic analysis of cox1 demonstrated its utility as a genetic marker for intra-specific differentiation. Furthermore, sequencing of the voltage-gated sodium channel (VGSC) gene revealed four key amino acid substitutions: T917I, I920F, V929R, and L930M. Notably, the T917I and I920F mutations have been previously linked to pyrethroid resistance in Pediculus humanus capitis, as well as in Bovicola and Haematopinus species. This suggests a similar potential for pyrethroid resistance in the H. tuberculatus populations examined in this study. These findings highlight the urgent need to implement integrated pest management (IPM) strategies that reduce reliance on pyrethroids and emphasize alternative control measures to safeguard buffalo health and productivity.

The ERF072 Transcription Factor Directly Regulates MtSOC1-Like Expression and Mediates Drought-Accelerated Flowering in Medicago truncatula

Flowering time is a key agricultural trait that indicates the yield of Medicago truncatula. Although drought stress affects flowering time in this species, the molecular mechanism underlying the enhancement of flowering to facilitate drought tolerance remains unclear. Accelerated flowering at the onset of drought enables drought escape in Medicago truncatula, ethylene-responsive factors are an important class of transcription factors whose members are involved in drought stress processes in numerous plants. In this study, MfERF072 overexpression accelerated flowering in Medicago truncatula. In addition, the knockdown of this gene did not affect flowering time, MfERF072 overexpression enhanced drought and decreased the flowering time of Medicago truncatula under drought stress. Moreover, a more pronounced phenotype was observed. In contrast, the knockdown of this transcription factor reduced drought tolerance and delayed flowering time. Furthermore, yeast one-hybrid and two-luciferase assays confirmed that ERF072 binds directly to the promoter of the flowering integration MtSOC1-like gene in Medicago truncatula. This consequently promotes floral transition under drought conditions. Our preliminarily data revealed that ERF072 regulates flowering under drought stress. These results may provide insights into new genetic resources for the molecular breeding of Medicago truncatula, ultimately supporting stress tolerance by balancing drought stress responses and flowering time.

Genetic diversity analysis and DNA fingerprinting of different populations of largemouth bass (Micropterus salmoides) in China with fluorescence-labeled microsatellite markers

BACKGROUND

Largemouth bass (Micropterus salmoides, LMB) is an economic fish in China, which has developed into many different cultured populations in the past decades. These populations exhibit different growth rates, morphological traits, stress resistance, and genetic diversity. Analyzing genetic diversity and molecular identification of these populations is crucial for conserving and utilizing germplasm resources, as well as for breeding new varieties.

RESULT

In this study, ten distinct LMB populations from China were collected and examined using fluorescence-labeled microsatellite markers. A total of 53 alleles were identified using seven microsatellite primer pairs, with allele counts ranging from 5 to 11 and an average of 7.571. The observed heterozygosity among the ten LMB populations varied from 0.210 to 0.967, while expected heterozygosity ranged from 0.204 to 0.651, and the polymorphism information content was between 0.175 and 0.597. Genetic distance varied from 0.019 to 0.457, the genetic differentiation index ranged from 0.013 to 0.258, and the number of effective migrants (Nm) was between 0.719 and 18.981. The genetic structure analysis indicated that the ten LMB populations could be classified into two or four groups. The analysis of molecular variance (AMOVA) revealed that 83.77% of genetic variation was found within individuals, with only 16.23% attributed to differences among populations. Through construction of DNA fingerprinting, we discovered unique fragments at several loci were detected in the populations such as the reintroduced Northern LMB population, "Youlu No.3" population, and the hybrid populations. Additionally, we also created digital DNA fingerprint maps of these LMB populations. Through analysis the digital DNA fingerprints from four candidate LMB populations, three known populations corresponded with the populations collected in this study. These results indicated high identification efficiencies of the digital DNA fingerprinting created in this study.

CONCLUSION

We established a method to distinguish 10 different LMB populations in China, which will assist in identification, traceability management, protection, and intellectual property rights of LMB in the future.

Fowl aviadenoviruses in Moroccan poultry: pathological characteristics and phylogenetic analysis of circulating fowl aviadenovirus strains from 2012 to 2024

Over the last decade, the emergence of aviadenovirus infections, namely inclusion body hepatitis (IBH) and gizzard erosion and ulceration syndrome (GEUS) have been occurring in Morocco with significant losses to the poultry industry. In this work, 255 suspected flock cases of IBH and GEUS were assessed among various poultry production types in the country from 2012 to 2024. Macroscopic pathological changes in affected chickens included an enlarged, discolored liver or a distended gizzard with haemorrhagic content and erosion/ulceration on the koilin layer. Microscopic findings revealed severe necrotic hepatitis, consistent with IBH, and/or necrotizing ventriculitis, which is characteristic of GEUS, with intranuclear viral inclusion bodies (INIB) in the hepatocytes or epithelial cells of the gizzard, which are attributable to fowl adenovirus (FAdV). The real time PCR results revealed that 71% (182/255) of the suspected FAdV cases tested positive. The prevalence varied by poultry production type, with broiler farms being the most affected at 79% (144/194), followed by layer farms at 15% (28/42), breeder farms at 5% (9/13), and turkey farms at 1% (1/6). Sequencing of the isolates identified FAdV serotype 11 (species D) and serotype 8b (species E) in 22 and 6 cases of IBH, respectively. Additionally, FAdV serotype 1 (species A) and serotypes 8a and 8b (species E) were detected in 9 and 2 cases of GEUS, respectively. These findings underscore the significant impact of fowl adenoviruses on the Moroccan poultry industry and highlight the need for continuous surveillance and targeted control interventions.RESEARCH HIGHLIGHTS Increase in FAdV infections (IBH and GEUS) in Morocco over past decade.FAdV-positive cases were mainly found in broiler farms (79%).Identification of FAdV-11 and 8b serotypes for IBH and FAdV-1, 8a and 8b for GEUS.

Analysis of Codon Usage Bias of 30 Chloroplast Genomes in Ulva (Ulvophyceae, Chlorophyta)

BACKGROUND

Ulva is a globally distributed genus with ecological and economic significance, yet the codon usage bias of the Ulva chloroplast genome remains poorly understood.

METHODS

We assessed the Ulva chloroplast genome codon usage patterns and their drivers by analyzing 30 genomes across 16 Ulva species.

RESULTS

The nucleotide composition analysis demonstrated that Ulva chloroplast genomes are rich in A/T, and prefer to use codons that ended with A/T. The relative synonymous codon usage analysis suggested that related species have similar codon usage patterns. A total of 25 high-frequency codons and 7-14 optimal codons were identified in these chloroplast genomes. The ENC values ranged from 31.40 to 32.76, all of which are less than 35, illustrating a strong codon bias of the Ulva genus. Our comparative analyses suggested that natural selection played the main role in the formation of the codon usage bias. Furthermore, the correlation analysis indicated that an influence of the base composition and gene expression levels on the codon usage bias.

CONCLUSIONS

This study provides the first comprehensive analysis of the codon usage patterns in Ulva chloroplast genomes, improving our understanding of the genetics and evolution of these economically and ecologically important macroalgae.

Nationwide Geographical and Temporal Distribution of Tick-Borne Diseases in Korean Water Deer (Hydropotes inermis argyropus)

Ticks are major vectors of numerous pathogens, and their public health significance is increasing due to climate change and the expanding involvement of wildlife hosts. In Korea, the Korean water deer (KWD, Hydropotes inermis argyropus) is widely distributed and considered a key wild host for ticks, potentially serving as a reservoir for diverse tick-borne diseases (TBDs). To examine the geographical and temporal distribution of TBDs in this species, 1035 spleen samples were collected from KWDs across 12 regions between April and November 2023. Overall, 93.6% (969) of samples were positive for at least one pathogen. Five Anaplasma species were identified: A. phagocytophilum, A. phagocytophilum-like A (APLA), APLB, A. bovis, and A. capra. In addition, Borrelia theileri and three Theileria species-T. capreoli, T. cervi, and T. luwenshuni-were detected. Notably, this study presents the first global detection of APLA, APLB, and B. theileri in KWDs. Statistically significant regional and seasonal differences in prevalence were observed, with higher detection rates in northern regions and during autumn, suggesting that environmental and ecological factors influence transmission dynamics. These findings highlight the role of KWD as a reservoir host for multiple TBDs and underscore the importance of wildlife-based surveillance for assessing zoonotic disease risks.

Agrotisvillenensis-a new species of Noctuinae (Lepidoptera, Noctuidae) from the southeastern Iberian Peninsula

Agrotisvillenensis sp. nov. is described from the Iberian Peninsula. Differential superficial, genital and genetic (barcode) characters from its closest Iberian and European relative species, Agrotisvestigialis (Hufnagel, 1766), are presented. Morphologically, the new species is best characterized in the male genitalia by the shape of the basal vesica and the presence of a median diverticulum and in the female genitalia by its comparatively long appendix bursae. The barcode of A.villenensis differs from those of related species and is assigned a unique BIN.

Screening optimum reference genes for quantitative real-time polymerase chain reaction analysis in black soldier fly Hermetia illucens under different conditions

With the completion of genome sequencing of the black soldier fly (BSF), an increasing number of researchers are focusing on elucidating its robust digestive and absorptive capabilities through genetic and molecular biology methods to enhance its growth performance. However, most genetic and molecular biology studies require gene expression analysis, and the stability of reference genes may change under different experimental conditions. To identify optimal reference genes, we evaluated 11 candidate reference genes (GAPDH, β-actin, GST, Tubulin α-1A, Tubulin α-4A, Tubulin β, RP49, RPL13, EF1-α, 18S RNA, and 28S RNA) across various developmental stages, tissues, sexes, and 3 distinct genotypes of Hermetia illucens using RefFinder software, which integrates the statistical algorithms geNorm, NormFinder, BestKeeper, and ΔCt. The results recommend that β-Actin, 18S RNA, and RPL13 are suitable for analyzing different developmental stages; RPL13, GST, and RP49 are optimal for different tissues; EF1, RPL13, and GST work best for different sexes; and RPL13, GAPDH, and 18S RNA are ideal for different genotypes. Notably, this study is the first to evaluate the stability of reference genes across 3 BSF genotypes originating from different regions. The findings offer valuable references and fresh insights for molecular biology research on H. illucens.

Molecular Characterization and Expression of the Ecdysone Receptor and Ultraspiracle Genes in the Wheat Blossom Midge, Sitodiplosis mosellana

20-hydroxyecdysone (20E) is essential for insect development and diapause. Ecdysone receptor (EcR) and ultraspiracle (USP) proteins are crucial regulators of 20E signaling. To explore their potential roles in the development of Sitodiplosis mosellana, a major wheat pest that undergoes obligatory diapause as a larva, one SmEcR and two SmUSPs (SmUSP-A and SmUSP-B) from this species were isolated and characterized. The deduced SmEcR and SmUSP-A/B proteins contained a conserved DNA-binding domain with two zinc finger motifs that bind to specific DNA sequences. Expression of SmEcR and the SmUSPs was developmentally controlled, as was 20E induction. Their transcription levels increased as the larvae entered pre-diapause, followed by downregulation during diapause and upregulation during the shift to post-diapause quiescence, which is highly consistent with ecdysteroid titers in this species. Topical application of 20E to diapausing larvae also elicited a dose-dependent expression of the three genes. Expression of SmEcR and SmUSPs decreased markedly during the pre-pupal stage and was higher in adult females compared to males. These findings suggested that 20E-induced expression of SmEcR and SmUSPs has key roles in diapause initiation and maintenance, post-diapause quiescence, and adult reproduction, while the larval-pupal transformation may be associated with a decrease in their expression levels.

De novo Biosynthesis of Caffeic Acid and Chlorogenic Acid in Escherichia coli via Enzyme Engineering and Pathway Engineering

Caffeic acid (CA) and chlorogenic acid (CGA) have diverse health benefits, including hemostatic, antioxidant, and antiinflammatory, highlighting their potential for medical applications. However, the absence of high-performance production strains increases production costs, limiting their wider application. In this study, we engineered Escherichia coli for the de novo production of CA and CGA. To improve production, a highly efficient mutant tyrosine ammonia-lyase from Rhodotorula taiwanensis (RtTALT415M/Y458F) was identified using genome mining and protein engineering. By engineering the tyrosine biosynthetic pathway through the deletion of pheA and tyrR, along with the overexpression of aroGfbr and tyrAfbr, we developed an engineered E. coli strain, CA11, which produced 6.36 g/L of CA with a yield of 0.06 g/g glucose and a productivity of 0.18 g/L/h. This represents the highest titer reported for microbial synthesis of CA using glucose as the sole carbon source in E. coli. Based on strain CA11, we further developed strain CGA13, with optimized replicons, promoters, and ribosome-binding sites, which produced 1.53 g/L of CGA in fed-batch fermentation, highlighting its potential for industrial-scale production.

Structural characteristics and anti-tumor activities of a novel polysaccharide from Klebsiella sp. SXW12

The purpose of this study is to elucidate the structure and biological properties of an extracellular polysaccharide (EPS), named EPS12, produced by Klebsiella sp. SXW12, a strain isolated from pond sludge. The maximum EPS12 yield of 15 g/L was obtained after optimizing the fermentation conditions by single-factor effects. EPS12 was an acidic homogeneous polysaccharide, and the molecular weight was measured to be 9.39 × 104 Da. Monosaccharide composition, methylation analysis, and NMR showed that EPS12 backbone was →3)-β-D-Glcp-(1 → 4)-β-D-GlcpA-(1 → 4) -α-L-Fucp-(1→, and terminal-β-D-Glcp was connected to the O-4 of →3)-β-D-Glcp-(1→. Network pharmacology analysis suggested that EPS12 may have anti-cancer effects. The anti-tumor effect of EPS12 on LLC-LUC tumor mice was studied. The results indicated that EPS12 exhibited excellent anti-tumor activity in mice at low doses (1, 2, and 4 mg/kg body weight). In vivo, EPS12 increased spleen index, promoted lymphocyte proliferation, and reduced spleen cell apoptosis through the Bcl-2-Bax/Bak-Caspase-3 apoptotic signaling pathway, and exhibited good biosafety. In addition, EPS12 could partially regulate the metabolic profiles of splenocytes. These properties make EPS12 a potential efficient and cost-effective anti-tumor agent or health product.

Genetic characterization and pathogenicity of two recombinant PRRSV-2 strains from lineages 1, 3, 5, and 8 emerged in China

BACKGROUND

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economic threat to the global swine industry. Currently, NADC30-like PRRSV has undergone complex recombination with local Chinese strains, which has exacerbated the evolution of PRRSV. Recently, new recombinant PRRSV-2 strains from four lineages (lineages 1, 3, 5, and 8) have emerged in China. However, information on the pathogenicity of the novel isolate in China remains limited. To further our knowledge about the isolate, FJLIUY2017 and PRRSV2/CN/G8/2018 were selected to analyze their pathogenicity for piglets.

METHODS

The PRRSV FJLIUY2017 and PRRSV2/CN/G8/2018 strains were isolated by porcine alveolar macrophages (PAMs) and MARC-145CD163. Complete genomic sequence analyses were conducted using the DNASTAR 7.0 software and the phylogenetic tree was constructed with MEGA 7.0. Recombination events were detected using RDP V4.10 and SIMPLOT software 3.5.1. Five PRRSV-free per group were inoculated with 2 mL (2 × 105 TCID50) of the FJLIUY-2017 and PRRSV2/CN/G8/2018. Clinical signs of disease were recorded daily after challenge. Blood samples were collected from all piglets on days 0, 4, 7, 11, and 14 dpi for analysis of viral load by IFA and PRRSV-specific antibody levels by ELISA kit. Lung gross and microscopic lesions of the inoculated piglets were examined by scoring system for lung lesion.

RESULTS

Full-length genome analysis revealed that FJLIUY2017 and PRRSV2/CN/G8/2018 share 89.2% identity with each other, and in particular, they had a low degree of homology (< 92%) with PRRSV sequences available in GenBank. Phylogenetic and recombination analyses revealed that the two strains were recombinant viruses from lineages 1, 3, 5.1, and 8.7 strains. Animal studies indicated that FJLIUY-2017 resulted in the typical clinical signs of PRRSV, including persistent fever, higher viremia, severe lung lesions, and 20% mortality, whereas PRRSV2/CN/G8/2018 caused moderate clinical symptoms and no mortality during the challenge period. Hyper-immune sera against the major vaccine strains JXA1-R (lineage 8) and Ingelvac PRRS MLV (Lineage 5) failed to neutralize two strains.

CONCLUSIONS

FJLIUY-2017 caused persistent fever, higher viremia, 20% mortality and exhibited higher pathogenicity in piglets compared to PRRSV2/CN/G8/2018. Our results suggest that recombination between different PRRSV-2 lineages can result in the development of PRRSV variants with increased pathogenicity.

Papiliomycessinensis (Clavicipitaceae) and Paraisariapseudoarcta (Ophiocordycipitaceae), two new species parasitizing Lepidopteran insects from southwestern China

Cordyceps sensu lato species are highly important for medicinal purposes and functional food nutrients. Two new species belonging to Cordyceps sensu lato are introduced, i.e., Papiliomycessinensis and Paraisariapseudoarcta. To comprehensively describe the significance of these two species, morphological data were supplemented with phylogenetic analyses based on six loci (nrSSU, ITS, nrLSU, tef-1α, rpb1, and rpb2). Phylogenetically, Pap.sinensis is most closely related to Pap.albostromaticus and Pap.shibinensis, yet it can be distinguished from them by its larger stromata (51.3-85.7 × 3.1-3.5 vs. 37.0-58.0 × 2.5-3.0) and longer phialides (10.1-26.9 × 0.9-3.3 vs. 9.8-24.3 × 1.5-3.1). Paraisariapseudoarcta is phylogenetically sister to Par.arcta. The longer stromata (43-51 vs. 16) and larger secondary ascospores (5.6-8.3 × 1.7-3.1 vs. 2.6-4.2 × 0.5-1.3) in Par.pseudoarcta are characteristics that distinguish the two species. A thorough morphological description and phylogenetic analysis of Pap.sinensis and Par.pseudoarcta were provided. In addition, taxonomic misconceptions of Par.gracilis (Ophiocordycipitaceae) were corrected.

Molecular Identification of Fusarium Isolates from Bozcaada Çavuş and Karalahna Grapes in Türkiye

Contamination of agricultural products by Fusarium species is a significant concern and is commonly found in various agricultural products. They cause severe economic losses in the products, and contaminate and threaten human and animal health due to the toxins they produce. Therefore, determining species diversity in various agricultural products is crucial. Bozcaada is well suited for cultivating the highest quality Çavuş grape due to its unique location and climate. Therefore, in this study, the sequencing of the tef1 and tub2 genes in Fusarium isolates from table Çavuş and wine grapes Karalahna, which are specific to Bozcaada, was performed, and their phylogenetic relationships were examined. As a result, it was determined that 11 of the 17 isolates were Fusarium annulatum from the Fusarium fujikuroi species complex (FFSC), 2 were Fusarium nirenbergiae from the Fusarium oxysporum species complex (FOSC), 2 were Fusarium fabacearum from the FOSC, and the last 2 isolates were Fusarium makinsoniae and Fusarium clavus (as 'clavum') from the F. incarnatum-equiseti species complex (FIESC). The F. makinsoniae and F. fabacearum species obtained in the study are the first recorded for Türkiye. This research highlights the variety of Fusarium species identified in Bozcaada vineyards in Türkiye.

Generation and Functional Characteristics of CRISPR/Cas9-Edited PtrPHOTs Triple-Gene Mutants in Poplar

Phototropins (PHOTs), as blue light receptors, play a pivotal role in plant light signal perception and adaptive regulation, yet their functional characteristics in trees remain poorly understood. In this study, the PHOT gene family was identified in Populus trichocarpa, and it included three members, PtrPHOT1, PtrPHOT2.1, and PtrPHOT2.2, all of which were highly expressed in mature leaves. Using CRISPR/Cas9 gene editing technology, triple-gene mutations in the PtrPHOT1/2.1/2.2 (PtrPHOTs) were generated, providing initial insights into the functions of PHOTs in trees. Compared to the wild type (WT), triple-gene ptrphots mutants displayed curved and wrinkled leaves, reduced leaf area, and delayed phototropic responses, indicating the central role of PHOTs in blue light signal perception. The stomatal aperture recovery rate in mutants was only 40% of that observed in WT, accompanied by significant downregulation of the BLUS1 gene transcription levels, confirming the conservation of the PHOT-BLUS1-H⁺-ATPase signaling axis in stomatal regulation. Transcriptome of triple-gene ptrphots mutants revealed 1413 differentially expressed genes, of which were enriched in auxin response (upregulation of SAUR family genes), jasmonic acid (downregulation of JAZ genes), and light signaling pathways, suggesting that PHOTs could regulate plant adaptability by integrating light signals and hormone homeostasis. Overall, this study achieved the knockouts of three PtrPHOTs family genes, and characteristics of triple-gene ptrphots mutants elucidated the multifunctional roles of PHOTs in leaf development, phototropism, and stomatal movement in poplar. Our work provides a foundation for deciphering light signaling networks and molecular breeding in woody plants.

Genome-Wide Identification of bZIP Gene Family in Lycium barbarum and Expression During Fruit Development

Wolfberry (Lycium barbarum L.) is a valued traditional medicinal plant and dietary supplement in China. The basic leucine zipper (bZIP) transcription factor (TF) family is a multifunctional group of regulatory proteins critical to plant biology, orchestrating processes such as growth and development, secondary metabolite biosynthesis, and stress responses to abiotic conditions. Despite its significance, limited information about this gene family in wolfberry is available. In this study, a total of 66 LbabZIP genes were identified, exhibiting a non-uniform distribution across all 12 chromosomes. Phylogenetic analysis divided these genes into 13 subgroups based on comparison with Arabidopsis bZIP proteins. Analysis of gene structures and conserved motifs revealed high similarities within individual subgroups. Gene duplication analysis indicated that dispersed duplication (DSD) and whole-genome duplication (WGD) events were the primary drivers of LbabZIP gene family expansion, with all duplicated genes subject to purifying selection. Cis-regulatory element (CRE) analysis of LbabZIP promoter regions identified numerous elements associated with plant growth and development, hormone signaling, and abiotic stress responses. Gene Ontology (GO) annotation further indicated that the LbabZIP genes are involved in transcriptional regulation, metabolism, and other biological processes. Transcriptome data and quantitative real-time PCR (qRT-PCR) analysis demonstrated tissue-specific expression patterns for several LbabZIP genes. Notably, LbaZIP21/40/49/65 showed significant involvement in wolfberry fruit development. Subcellular localization assays confirmed that these four proteins are nucleus-localized. This comprehensive analysis provides a theoretical foundation for future studies investigating the biological functions of LbabZIP genes, especially their role in wolfberry fruit development.

Genome wide identification and functional analyses of HAK family potassium transporter genes in passion fruit (Passiflora edulis Sims) in response to potassium deficiency and stress responses

The nutritional status of potassium directly affects the yield and quality of fruits. The molecular mechanism underlying K+ uptake and transport in passion fruit (Passiflora edulis Sims), particularly under K+ limited conditions, remains poorly understood. Members of the high-affinity K+ (HAK) transporter family play a vital role in K+ acquisition, translocation, and stress responses. However, the biological functions of these genes in passion fruit plants are still unknown. This study identified 14 HAK genes (PeHAKs) in Passiflora edulis genome. Phylogenetic analysis classified these PeHAKs into three distinct clusters containing 9, 4, and 1 genes, respectively, with conserved structural features supporting their functional divergence. Promoter analysis revealed 12 predominant cis-acting elements, including hormone-responsive, stress-inducible, and core transcriptional regulatory motifs. Tissue-specific expression profiling demonstrated significant organ-dependent expression patterns of PeHAKs across roots, stems, leaves (young/mature), flowers, and fruits. Under K+ deficiency, salinity stress, and phytohormone treatments, the transcript levels of PeHAKs were significantly altered in roots and leaves. Notably, PeHAK10 exhibited dual induction in aerial and subterranean tissues under K+ deprivation. Functional complementation assays in yeast validated the K+/Na + transport activity of PeHAK10, suggesting its involvement in ion homeostasis regulation during nutrient stress. This study provides the first genome-wide characterization of the PeHAKs family of genes in passion fruit plants, establishing a foundation for elucidating their biological roles in potassium nutrition regulation and stress adaptation.

Functional analysis of AobHLH88 involved in anthocyanin synthesis using multi-omics data in Asparagus officinalis

Basic helix loop helix (bHLH) proteins play critical functions in various aspects of plant growth and development, especially in anthocyanin synthesis. Although the Asparagus genome has been sequenced, there is limited information on the bHLH gene family within this species. This study identifies 96 AobHLH transcription factor genes in the Asparagus genome. Chromosomal localization indicated 91 AobHLHs across nine chromosomes. Phylogenetic analysis categorized them into nine distinct subfamilies, each with specific motif characteristics. Synteny analysis showed that both dispersed duplication and whole-genome or segmental duplications contributed to the expansion of AobHLHs, identifying 19 orthologous pairs between Asparagus and Arabidopsis. Differential expression analysis indicated a notable increase in AobHLH10, AobHLH18, and AobHLH88 gene expression during anthocyanin synthesis, as shown in Asparagus RNA-seq data. Among them, AobHLH88 displayed the higher differential expression pattern in 'Purple Passion'. Subcellular localization analysis displayed that AobHLH88 was localized in the nucleus. Furthermore, overexpression of AobHLH88 in tobacco plants highlighted its significant role in enhancing anthocyanin accumulation in Asparagus spear color. Collectively, this in-depth identification and characterization of AobHLH gene family members establish a foundational resource for future investigations on the molecular mechanism involvement of bHLH genes in Asparagus.

Prevalence and zoonotic potential of pathogens in micromammals (rodents and insectivores) in the Republic of Korea

Micromammals (rodents and insectivores), are reservoirs of numerous zoonotic pathogens and play a critical role in infectious disease transmission. The rising prevalence of micromammals-associated pathogens in the Republic of Korea highlights the urgent need for targeted surveillance. Here, we analyzed micromammal blood samples collected from 16 nationwide sites during spring 2022, autumn 2022, and spring 2023 to investigate the following key zoonotic diseases: severe fever with thrombocytopenia syndrome, Lyme disease, Q fever, scrub typhus, anaplasmosis, ehrlichiosis, and rickettsioses. Our analysis revealed that of the 756 micromammal samples analyzed, 0.1 % had Borrelia afzelii, Borrelia valaisiana, and Orientia tsutsugamushi, 12.7 % contained Anaplasma phagocytophilum, and 82 % Neoehrlichia mikurensis. Importantly, we detected Borrelia valaisiana in micromammals in the Republic of Korea for the first time. Phylogenetic analysis identified close genetic links between local and global pathogen strains, highlighting potential cross-border transmission risks. The high prevalence of Neoehrlichia mikurensis emphasizes the zoonotic threat of micromammals. These findings provide crucial insights about enhancing micromammals-associate pathogen surveillance, inform public health strategies, and reinforce the importance of monitoring micromammal populations for zoonotic infection risk mitigation in Korea and beyond.

Molecular Profiling and Pathological Evaluation of Bovine Papillomavirus-1 in Cattle in Al-Sharkia, Egypt

Bovine papillomatosis virus (BPV) is a prevalent cutaneous oncogenic viral disease in cattle, causing economic losses due to reduced milk production, poor carcass quality, and hide damage. Despite BPV's economic significance, molecular information on current strains, genetic relationships, and origins in Egypt is limited, with most studies focusing on electron microscopy and histopathological analysis. The study aimed to genetically analyze BPV-1 circulation in Al-Sharkia, Egypt, and characterize viral strains compared with local and global papillomaviruses isolates. A total of 27 crossbred cattle with clinical symptoms of papillomatosis, such as wart-like lesions on various body parts, were examined. The collected tissue samples underwent histological analysis, revealing typical benign neoplasms such as hyperkeratosis and koilocytes. Polymerase chain reaction (PCR) confirmed the presence of BPV-1 in all samples, with partial amplification of the L1 gene. Sequencing and phylogenetic analysis of three representative samples indicated high similarity to BPV-1 strains from Egypt, Iraq, Turkey, and Belgium, suggesting livestock trading may play a role in disease transmission. The isolates were found to be linked to equine Delta papillomavirus 4 (DPV4) strains, indicating cross-species transmission between cattle and equines. The study marks one of the first reports of BPV-1 infection in cattle in Al-Sharkia, providing crucial molecular insights into Egypt's circulating strains and emphasizing the need for stronger biosecurity protocols in animal trading.

Molecular characterization and functional analysis of IL-18 in large yellow croaker (Larimichthys crocea)

Interleukin-18 (IL-18), a pro-inflammatory cytokine of the IL-1 family, is crucial for protecting the host against pathogen infection in mammals. In this study, a IL-18 homolog gene was cloned from large yellow croaker (Larimichthys crocea) (LcIL-18), which has an open reading frame (ORF) of 609 bp that encodes a polypeptide of 202 amino acids. The LcIL-18 C-terminus contains a typical IL-1 family signature and a caspase cleavage site. Phylogenetic analysis showed that LcIL-18 was most closely related to IL-18 of Miichthys miiuy. It was found that LcIL-18 was constitutively expressed in all 12 tissues tested of large yellow croakers, with the highest expression in gills. The expression of LcIL-18 in head kidney, spleen, skin, gills, and liver showed a differential pattern following infection with Pseudomonas plecoglossicida and Vibrio alginolyticus. P. plecoglossicida strongly induced LcIL-18 expression in these tissues. Conversely, in the early stage of infection, V. alginolyticus significantly inhibited LcIL-18 expression in head kidney, spleen, skin, and gills, but not in the liver. In vitro, LPS, Poly(I:C), P. plecoglossicida, and V. alginolyticus significantly upregulated the expression of the LcIL-18 in large yellow croaker head kidney (LYCK) cells. Furthermore, recombinant LcIL-18 (rLcIL-18) significantly increased cell viability and upregulated the expression of pro-inflammatory cytokines (LcIL-1β, LcIL-6, and LcTNF-α1) in LYCK cells. Our findings therefore indicated that LcIL-18 was involved in pro-inflammatory response induced by pathogenic bacteria.

A full-length S1 gene sequencing of a novel emerged GI-19 and GI-23 lineages of Infectious bronchitis virus currently circulating in chicken flocks in upper Egypt reveals marked genetic diversity and recombination events

BACKGROUND

Infectious bronchitis virus (IBV) is a highly contagious evolving pathogen that causes respiratory, urinary and reproductive symptoms; threatening the poultry industry globally.

METHODS

During this study, 90 tissue specimens were collected from various poultry flocks of seven Upper Egypt governorates from 2023 to 2024 for genetic characterization.

RESULT

Typical IBV lesions of the inoculated embryos in the specific-pathogen-free-embryonated chicken eggs (SPF-ECE) were observed. Using real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay targeting the conserved N gene, only 60 samples were considered positive with 66.6%. Collectively, 23 tissue specimens were examined through a one-step PCR assay. Sequencing is targeting the S1 gene, and the phylogenetic analysis was conducted based on partial sequencing showed that Avian coronavirus (ACoV) isolates belong to GI-23 (n = 18), GI-12 (n = 2), GI-1 (n = 1), and GI-19 (n = 2). Genotyping of the S1 gene indicates that GI-23 shows a genetic similarity to Egyptian isolates, and Israeli variants with nucleotide identity percentages (95-97%) and, (88-92%); respectively. Concerning full sequencing, five ACoV isolates were clustered as GI-23 (n = 3), and GI-19 (n = 2). Currently, QX-strains showed low genomic relatedness with Egyptian strains, and vaccinal strains with nucleotide (78-79%), and amino acid (77-80%), and (75-77%) identities, respectively. This is the first detailed study that recorded various IBV isolates, especially the novel emerged QX strain circulating in chicken flocks in Egypt. The recombination event within the Assuit-1-QX-EGYIBV-2024 isolate was detected as a result of recombination between the major (GI-19) and minor (GI-22) putative parents. Importantly, the G1-19 and G1-23 shared multiple amino acids mutations at S1 gene.

CONCLUSIONS

This study provides empirical evidence for the ACoV circulating in Egypt in vaccinated and non-vaccinated poultry flocks despite the excessive vaccination schemes.

Paracorymbiglomus gen. nov., Diversisporaconica sp. nov., and new combinations in Diversisporaceae (Glomeromycota)

The paper presents the results of morphological studies, as well as comparisons and phylogenetic analyses of sequences of the 45S (= 18S-ITS-28S) nuc rDNA region and the rpb1 gene (when available) of four arbuscular mycorrhizal fungi (AMF) of the phylum Glomeromycota. These fungi were (i) an informally named isolate 449, suspected of being an undescribed species of the genus Diversispora, and (ii) three Corymbiglomus species in the family Diversisporaceae. The studies confirmed the novelty of isolate 449 in Diversispora and showed that Corymbiglomus contains only C.corymbiforme, while C.globiferum and C.pacificum should be transferred to a separate genus sister to Corymbiglomus. Consequently, isolate 449 was described as Diversisporaconica sp. nov., C.globiferum, and C.pacificum were placed in Paracorymbiglomus gen. nov. and renamed P.globiferum comb. nov. and P.pacificum comb. nov.

Taxonomy and phylogeny of entomopathogenic fungi from China-revealing two new genera and thirteen new species within Clavicipitaceae (Hypocreales, Ascomycota)

Scale insects (Coccidae, Hemiptera) and whiteflies (Aleyrodidae, Homoptera) are diminutive, ubiquitous, sap-sucking plant parasites, many of which are serious agricultural pests. Over the course of several years, an investigation into entomopathogenic fungi affecting scale insects and whiteflies resulted in the collection of 13 novel species of Clavicipitaceae in Yunnan and Hainan Provinces, China. Based on three-loci (nrLSU, tef-1a, and rpb1) phylogenetic analysis and morphological evidence, it was determined that two new genera, Paramoelleriella and Polymicrospora, each encompassed a new species. Additionally, two new species of Hypocrella s. str. and nine new species of Moelleriella were identified. Within the Moelleriella clade, seven new species were assigned to the Effuse clade and two to the Globose clade. Hypocrella s. str. and Samuelsia were included in the Pulvinate clade, to which the new genus Paramoelleriella is closely related, although it forms a distinct branch. Paramoelleriella species exhibited characteristics similar to those of Moelleriella, including globose to subglobose, yellow to orange teleomorphic stromata, with perithecia densely arranged and fully embedded in the stromatal tissue. Its ascospores disarticulated into short-cylindrical part-spores, and the conidiomata featured large, widely open orifices bearing fusoid conidia curved to one side. Species of the new genus Polymicrospora were characterized by thin-pulvinate, snow-white to off-white teleomorphic stromata with surface smooth. These species possessed numerous obpyriform or oval, semi-embedded, and densely arranged perithecia, cylindrical asci, and ascospores that disarticulated into small, oval part-spores in large quantities. This study introduces two new genera and 13 new species, accompanied by detailed illustrations and descriptions.

Mycological and molecular identification of mycoses involved in mastitis from Holstein dairy cattle with special reference to Candida albicans

Globally, mastitis is an incredibly devastating, multifactorial disease that affects the dairy industry. However, cases of mycotic mastitis in dairy cows have increased in recent years. This study aimed to investigate the prevalence of mycotic mastitis with special reference to Candida albicans in Holstein-Friesian dairy cows from some farms in Menoufia province, Egypt. For the study, 150 milk samples (n = 150, 20 from healthy cows and 130 from cows with subclinical and clinical mastitis) were collected from 15 smallholder dairy farms located in three localities (Quesina, Elbagour, and Shibin El-Kom) five farms from each. The samples were subjected to mycological culture and subsequently verified using traditional morphological and biochemical tests to confirm fungal characteristics followed by antimycotic susceptibility testing using Vitec 2 system. Finally, molecular identification was carried out via PCR and phylogenetic analysis. 27 samples out of 130 were positive for fungal culture representing (20.77%). Candida species were recorded the highest percentage (62.96%) of the detected fungi (17/27). In addition, C. albicans was the predominant species (3/27), which corresponds to 11.11%. Antifungal susceptibility testing of the fungal isolates showed the highest susceptibility to micafungin, followed by caspofungin (88.88% and 86.19%, respectively). However, the lowest susceptibility was noted against amphotericin B (50.55%). The three isolates of C. albicans were confirmed by PCR by amplifying the ITS region, which was then sequenced for phylogenetic analysis. The sequences have been deposited in GenBank under the following accession numbers: OR97266, OR97267, and OR97268. Our results indicate that Candida spp., especially C. albicans, is one of the major causes of mycotic mastitis in dairy cows in Egypt. Moreover, micafungin might be the efficient medication for treating these cases of mycotic mastitis, followed by caspofungin.

Secalonic acid F1 derived from an endophytic fungus Periconia verrucosa as a potential antimicrobial agent against Staphylococcus aureus

AIM

To investigate the antimicrobial potential of a secalonic acid F1 derivative produced by an endophytic Periconia verrucosa.

METHODS AND RESULTS

The endophyte RDE85 was characterized as P. verrucosa by morphological and phylogenetic analysis. We characterized a major compound from RDE85 as Secalonic acid F1 (SF1) with a 2,4'-linkage. SF1 demonstrated antimicrobial activity with an IC50 of 7.6 µg mL-1 against Staphylococcus aureus. It inhibited the biofilm formation, causing morphological changes and disruption of cell membrane integrity in the pathogen, confirmed by scanning electron microscopy (SEM). The compound depicted strong synergistic potential with ciprofloxacin and reduced DNA and RNA synthesis. The time-kill kinetics demonstrate that SF1 is an effective concentration-dependent bactericidal agent. Further, SF1 severely affected the respiratory chain dehydrogenase activity, confirmed by in-silico studies, revealing its interaction with respiratory chain succinate dehydrogenase. The treatment with this compound downregulated the staphylococcal accessory gene regulator and enterotoxin gene, two important virulence factors of the organism, and reduced the staphyloxanthin production, which is also an important virulence trait.

CONCLUSION

SF1 is a potential antimicrobial agent against S. aureus.

First report of highly pathogenic Theileria luwenshuni in Sri Lanka: Are Jaffna sheep resistant to theileriosis?

Theileriosis is a tick-borne piroplasmid infection that affects small ruminant production, resulting in significant economic losses. This study investigated theileriosis and its potential vectors in the Jaffna sheep breed in Sri Lanka. Blood (n = 100) and ticks (n = 57) were randomly collected from three farms. Management practices and other demographic data were collected using a questionnaire. Giemsa-stained blood smears facilitated microscopic analysis of piroplasms. The prevalence of theileriosis was compared between farms, age, and gender categories using a Chi-square test or a Fisher's exact test. The molecular identification was achieved using a nested PCR targeting the 18S rRNA gene of Theileria spp. Subsequently, PCR amplicons were subjected to bidirectional sequencing and phylogenetic analysis. Microscopic examination and nested PCR revealed 38.0 % and 90.9 % prevalence of Theileria species, respectively, with a significant difference (p = 0.0015). The phylogenetic analysis showed that the Theileria spp. identified is the highly virulent Theileria luwenshuni. Collected tick species were: Haemaphysalis bipsinosa, Haemaphysalis intermedia, Rhipicephalus haemaphysaloides, Rhipicephalus linneai and Hyalomma marginatum isaaci; the most prevalent being H. bispinosa (68.4 %). This is the first report and molecular characterisation of T. luwenshuni in Sri Lanka, a highly pathogenic species recorded in small ruminants in tropical and subtropical countries but does not cause clinical signs in the Jaffna sheep breed. Findings of the current study suggest that Jaffna sheep tolerate the infection by T. luwenshuni. However, them being carriers poses a major risk to immunocompromised farm animals, especially the exotic sheep and goat breeds in the country.

Exploring Mitonuclear Discordance: Ghost Introgression From an Ancient Extinction Lineage in the Odorrana swinhoana Complex

Mitonuclear discordance, the incongruence between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA), is a well-documented phenomenon with various potential explanations. One emerging hypothesis, ghost introgression, refers to the genetic contribution of an ancient, extinct or unsampled lineage and can now be tested using modern genomic data and demographic models. In this study, we investigated the evolutionary history of the Odorrana swinhoana complex (Anura: Ranidae), which includes O. swinhoana, O. utsunomiyaorum and an unidentified population with highly divergent mtDNA. While mitochondrial phylogeny suggested this population as a basal lineage, nuclear data from ddRADseq revealed it as a mixture of the most derived O. swinhoana nuclear sequences combined with ancient mtDNA. Demographic modelling further supported ghost introgression, as all models incorporating a ghost population outperformed those without it. These findings suggest that an eastward expansion of western O. swinhoana replaced an ancient Odorrana lineage, leaving only its mtDNA and fragments of its nuclear genome in the hybrid population. Our results provide one of the first documented cases of ghost introgression in amphibians and highlight its potential as a widespread evolutionary process. This study also underscores the risks of relying solely on mtDNA for phylogenetic reconstruction and species delimitation.