Phylogenetic Tree Analysis Research Articles

Genome wide identification of Dof transcription factors in Carmine radish reveals RsDof33 role in cadmium stress and anthocyanin biosynthesis

Carmine radish (Raphanus sativus L.) is cultivated in Fuling, Chongqing, for its red color. Dof-TFs are critical in regulating plant growth, development, stress responses, and signal transduction.This work comprehensively examined the structure, evolution, and expression of the carmine radish Dof gene and its behavior under cadmium (Cd) stress. The radish genome has 59 RsDofs, which are divided into nine clusters (A: 8, B1: 10, B2: 10, C1: 3, C2.1: 5, C2.2: 4, C3: 11, D1: 4, and D2: 4). Phylogenetic tree analysis revealed significant Dof gene family resemblance between Arabidopsis thaliana and Brassica napus. Perhaps segment duplication resulted in RsDof gene family expansion. Cd stress-induced RsDof expression patterns were studied using an RNA-seq atlas and qRT-PCR. The majority of RsDofs were tissue-specific and Cd-sensitive. The involvement of RsDof genes in Cd stress response and anthocyanin synthesis was verified using qRT-PCR. RsDof33 is involved in Cd stress response and anthocyanin synthesis. A. thaliana overexpressed the recombinant fusion protein RsDof33-GFP, which was localized to the nucleus, resulting in fewer rosette leaves, delayed flowering, and higher anthocyanin concentration. RsDof33-expressing plants had significantly higher transcript levels of the auxin biosynthetic genes YUCCA (AtYUC2), auxin efflux carrier (AtPIN4), and AtKNAT2, which are involved in leaf shape development, as well as AtPAL, AtCHS, AtCHI, AtDFR, AtLDOX, and AtUF3GT. These findings indicate that RsDofs are critical to plant development and stress responses.

The first complete mitochondrial genome sequence of the common Baya weaverbird (Ploceus philippinus) from southern India

The common Baya weaverbird, Ploceus philippinus (Linnaeus, 1766), is best known for its nest construction behaviour. Yet, no genomic studies have been conducted on this species to date. We sequenced the mitochondrial genome of P. philippinus sampled from southern India. The circular mitochondrial genome of 16,867 bp contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs (12S and 16S subunits), and a non-coding control region. A maximum-likelihood phylogenetic tree analysis placed P. philippinus and P. nigricollis weaverbirds in a separate clade among other bird species. The mitochondrial genome sequence would benefit future genetic studies in weaverbirds.

Genome-Wide Identification of Wheat USP Gene Family and Functional Dissection of TaUSP85 Involved in Heat Tolerance

A collection of conserved proteins known as universal stress protein (USP) is present in a wide range of species, including plants, fungi, bacteria, and animals. USPs are named for their ability to respond to a variety of stress conditions, such as heat stroke, osmotic stress, nutrient limitation, and exposure to toxins or antibiotics. While the USP response to different stress conditions in plants has been reported, little is known about the USP family in wheat (Triticum aestivum L.). In wheat, we identified 88 USP genes distributed across 21 chromosomes classified into four subfamilies. Phylogenetic tree and synteny analysis across multiple species revealed a highly conserved evolution of the USP family between monocots and dicots. Based on comparative analysis of protein domains, gene structure and conserved motifs, TaUSPs showed significant differences among the four subfamilies. Furthermore, expression pattern analysis of TaUSPs showed significant differences among various tissues and under different abiotic stress conditions. We further conducted transformation experiments with the TaUSP85 gene, which significantly enhanced yeast thermotolerance. Silencing of TaUSP85 through VIGS experiments in wheat resulted in significant wilting, decreased chlorophyll content, and increased MDA accumulation compared to control plants. The silenced plant lines had much more ROS accumulation than the control group, as determined by the findings of DAB and NBT staining. The interaction proteins TaUSP1 and TaUSP11 of TaUSP85 were screened by yeast two-hybrid and their interaction relationship was further verified by LCI. Overall, our findings enhance the comprehension of the USP gene family in wheat and provide a valuable resource for further investigation of these genes in wheat and related cereal crops.

Batch fermentation and GC-MS analysis of biocontrol agent, Bacillus amyloliquefaciens strain KSAS6 and its impact on soilborne fungus, Sclerotium bataticola

Background: Sclerotium bataticola, a soil-born fungus, is responsible for charcoal rot in a variety of plants. It is also responsible for causing substantial damage to a wide range of horticultural crops around the world.Methods: Fifteen different Bacillus isolates were isolated and evaluated for their ability to inhibit S. batatacola's growth. The promising bacterial isolate was molecularly identified using NCBI-Blast and phylogenetic tree analysis of the 16S rRNA gene. Batch fermentation was performed in a stirred tank bioreactor to maximize culture biomass and secondary metabolite synthesis. Gas chromatography-mass spectrometry was used to discover secondary metabolite compounds.Results: The KSAS6 isolate was the most effective for inhibiting the fungal growth of mycelial cells, with a 48.2% inhibition percentage. The probable biocontrol agent, B. amyloliquefaciens strain KSAS6, was identified and recorded in GenBank under the accession number PQ271636. The culture biomass and secondary metabolites were maximized by the batch fermentation technique, reaching the highest achievable level of 2.1 g L-1 at 11 hours. This was accomplished while maintaining a steady specific growth rate (µ) of 0.13 h-1. Based on the observations, the biomass yield coefficient was found to be 0.37 g cells/g glucose. Among the 21 secondary metabolite compounds identified in GC-MS analysis, diisooctyl phthalate was the highest compound (43.31%).Conclusion: The strain of rhizobacterium B. amyloliquefaciens known as KSAS6 can inhibit the growth of S. bataticola, which makes it a promising candidate for the biocontrol of fungal infections in plants.Keywords: Sclerotium bataticola; Bacillus amyloliquefaciens; Batch fermentation; Secondary metabolites; antifungal

Isolation and characterization of a novel highly efficient bacterium Lysinibacillus boronitolerans QD4 for quantum dot biosynthesis

Microorganism-based biosynthesis of quantum dots is a low-cost and green production method with a wide range of potential applications. The development of environmentally friendly synthesis methods is required due to the toxicity and severe reactions that occur during the chemical synthesis of quantum dots. In this study, a novel strain, QD4, with the ability to the effectively and rapidly biosynthesize CdS quantum dots, is isolated and reported. The isolated strain is a Gram-positive, aerobic, flagellated, and rod-shaped bacterium, isolated from seawater. Through the physio-biochemical characterization and 16S rRNA-based phylogenetic tree analysis, the strain is identified as Lysinibacillus boronitolerans QD4. The strain QD4 grows well in the range of 25–40 °C (optimum, 37 °C), pH 5.0–9.0 (optimum, pH 7.0), with a high cadmium-resistance as it could grow at Cd2+ concentration up to 2 mM, implying its good adaptability to the environment and potential for application. Cd2+ and L-cysteine are used as substrates for the biosynthesis of CdS quantum dots by strain QD4. The distinctive yellow fluorescence from CdS quantum dots is visible after only a short induction time (a few hours). Moreover, the properties of the CdS quantum dots are characterized by fluorescence spectroscopy, UV-absorption spectroscopy, TEM, XRD, XPS, and infrared spectroscopy. This study provides a novel strain resource for efficient biosynthesis of extracellular, water-soluble quantum dots, paving potential industrial applications in green production.

Engineering Saccharomyces cerevisiae for growth on xylose using an oxidative pathway

The fermentative production of valuable chemicals from lignocellulosic feedstocks has attracted considerable attention. Although Saccharomyces cerevisiae is a promising microbial host, it lacks the ability to efficiently metabolize xylose, a major component of lignocellulosic feedstocks. The xylose oxidative pathway offers advantages such as simplified metabolic regulation and fewer enzymatic steps. Specifically, the pathway involves the conversion of xylose into 2-keto-3-deoxy-xylonate, which can be channeled into two distinct pathways, the Dahms pathway and the Weimberg pathway. However, the growth of yeast on xylose as the sole carbon source through the xylose oxidative pathway has not been achieved, limiting its utilization. We successfully engineered S. cerevisiae to metabolize xylose as its sole carbon source via the xylose oxidative pathways, achieved by enhancing enzyme activities through iron metabolism engineering and rational enzyme selection. We found that increasing the supply of the iron-sulfur cluster to activate the bottleneck enzyme XylD by BOL2 disruption and tTYW1 overexpression facilitated the growth of xylose and the production of ethylene glycol at 1.5 g/L via the Dahms pathway. Furthermore, phylogenetic analysis of xylonate dehydratases led to the identification of a highly active homologous enzyme. A strain possessing the Dahms pathway with this highly active enzyme exhibited reduced xylonate accumulation. Furthermore, the introduction of enzymes based on phylogenetic tree analysis allowed for the utilization of xylose as the sole carbon source through the Weimberg pathway. This study highlights the potential of iron metabolism engineering and phylogenetic enzyme selection for the development of non-native metabolic pathways in yeast.Key points• A 1.5 g/L ethylene glycol was produced via the Dahms pathway in S. cerevisiae.• Enzyme activation enabled growth on xylose via both the Dahms and Weimberg pathways.• Tested enzymes in this study may expand the application of xylose oxidative pathway.

Revealing a novel GI-19 lineage infectious bronchitis virus sub-genotype with multiple recombinations in South Korea using whole-genome sequencing.

Infectious bronchitis (IB), caused by the infectious bronchitis virus (IBV), is a highly contagious chicken disease, causing economic losses worldwide. New IBV strains and variants continue to emerge despite using inactivated and live-attenuated vaccines to prevent or control IB. In this study, the S1 genes of 46 IBV strains, isolated from commercial chicken flocks between 2003 and 2024 in Korea were sequenced and genetically characterized. The IBV isolates belonged to Korean group II (K-II), which was included in the GI-19 lineage. The K-II was divided into five sub-genogroups (a-e) based on phylogenetic tree analysis results and nucleotide identification of the S1 gene. Of these, K-IId was the most common genotype in Korea; however, eight novel isolates belonging to the K-IIe sub-genotype were discovered. The nucleotide and amino acid identities of the other four K-II sub-genotypes and the eight isolates were 84.42-95.89% and 84.02-95.86%, respectively. The complete genomes of the eight K-IIe isolates were obtained using next-generation sequencing. Various recombination patterns were observed despite the high homology of the S1 gene among the eight IBV strains. Among the eight K-IIe isolates, six were recombinants, exhibiting recombinations between K-IIe and K-IIc, K-IIe and K-IIa, and with the live vaccine strain. Most recombination breakpoints were detected in the nsp2 region of the ORF1a, S2, and M genes. The present study proposed new classification criteria for the K-II belonged to the GI-19 lineage prevalent in South Korea and revealed the recombination patterns of recently identified novel isolates, providing important information on novel viral sub-genotype strains and IBV evolution.

Diagnosis and molecular characterization of three allexiviruses infecting garlic crop in Saudi Arabia.

Forty-four samples of garlic plants showing virus-like symptoms were collected, during the growing season (2021-2022) from different locations in Qassim province, Saudi Arabia. These samples were analyzed by ELISA against the important Allium allexiviruses including garlic virus A (GarV-A), garlic virus B (GarV-B), garlic virus C (GarV-C), and Shallot virus X (ShVX). The obtained results showed that 22/44 (50%) samples were found to be infected with one of the tested viruses. Mixed infections were detected in 13/22 samples (59.1%) with more than one virus. However, 13.6%, 0% and 27.2% were detected as single infection with GarV-A, GarV-B and GarV-C respectively. RT-PCR amplification with general allexiviruses primer (750 bp) and specific primers for GarV-A (1330 bp), GarV-B (1216 bp) and GarV-C (1557 bp) were used to detect the respective viruses. The phylogenetic tree and nucleotide sequence analysis of one of each GarV-A (OQ397541), GarV-B (OQ397542) and GarV-C (OQ397543) with general primer for allexiviruses while one isolate of each GarV-A (ON155441), GarV-B (OR343811) and two isolates of GarV-C (ON155445, and ON155446) with specific primers showed their similarity with their respective viruses from GenBank. In host range study, Chenopodium amaranticolor, Nicotiana benthamiana, N. tabacum and Allium cepa expressed necrotic lesions, mosaic and yellowing symptoms respectively against GarV-A, GarV-B and GarV-C. To our knowledge, this is the first report of GarV-A, GarV-B, and GarV-C in Saudi Arabia.

Population Genetics of Haliotis discus hannai in China Inferred Through EST-SSR Markers.

The Pacific abalone Haliotis discus hannai originated in cold waters and is an economically important aquaculture shellfish in China. Our goal was to clarify the current status of the genetic structure of Pacific abalone in China. In this study, eighteen polymorphic EST-SSR loci were successfully developed based on the hemolymph transcriptome data of Pacific abalone, and thirteen highly polymorphic EST-SSR loci were selected for the genetic variation analysis of the six populations collected. The results showed that the average number of observed alleles was 8.0769 (RC)-11.3848 (DQ) in each population. The number of observed alleles in the DQ, NH, and TJ populations was significantly higher than that in the RC population. The cultivated population outside the Changshan Islands has experienced a 22.79% reduction in allele diversity compared to the wild population of DQ. The pairwise Fst values and analysis of molecular variance (AMOVA) revealed significant population differentiation among all populations except DQ and NH populations, with RC and ZZ cultured populations exhibiting the largest population differentiation (Fst = 0.1334). The phylogenetic tree and structural analysis divided the six populations into two groups (group 1: NH, DQ, and ZZ; group 2: DL, TJ, and RC), and there was no relationship between geographical distance and genetic distance. These results may reflect the large-scale culture from different populations in China and the exchange of juveniles between hatcheries. Different breeding conditions have led to a higher degree of genetic differentiation between the RC and ZZ populations. This study enables a better understanding of the genetic diversity and structure of current Pacific abalone populations.

Isolation, identification and characteristics of Aeromonas sobria from diseased rainbow trout (Oncorhynchus mykiss).

Aeromonas sobria is an opportunistic pathogen that can infect humans, animals and aquatic species, which is widely distributed in different aquatic environments and products. In recent years, with the rapid expansion of intensive aquaculture, the disease caused by A. sobria has occurred. This study aims to understand the pathogenic characteristics of A. sobria and provide scientific basis for the prevention and control of the epidemic. The dominant strain As012 was isolated from the diseased rainbow trout during the outbreak. Through physiological and biochemical experiments, sequencing and phylogenetic tree analysis of 16S rRNA and gyrB genes, the strain As012 was identified as A. sobria. The clinical signs of the diseased rainbow trout in the experimental infection were consistent with those in the farm, and the LD50 was 1.0 × 106.6 CFU/mL. The histopathological lesions in the gills, heart, liver, spleen and intestines were mainly extensive hemorrhage. In addition, eight virulence genes were screened from strain As012, including Act, Aer, AexT4, Alt, ahyB, ascV, Nuc and Hly. The strain As012 can grow in the environment with pH 1-11, temperature 8-43°C and NaCl concentration 0-8%. The drug sensitivity results showed that it was resistant to 12 antibiotics including penicillin G, vancomycin, and clindamycin, and highly sensitive to 16 antibiotics including cefazolin, ciprofloxacin, and furadantin. The results showed that A. sobria, the dominant strain isolated from diseased rainbow trout, was the main pathogen causing the epidemic in the farm. The strain As012 has a very wide range of growth and strong pathogenicity, causing widespread hemorrhaging in various tissues of rainbow trout. It is multi-resistant, but highly sensitive to cephalosporins, quinolones, nitrofurans and sulfonamides. Among them, ciprofloxacin will be one of the effective antibiotics for preventing and controlling A. sobria infection in Chinese aquaculture.

Overexpression of AtruLEA1 from Acer truncatum Bunge Enhanced Arabidopsis Drought and Salt Tolerance by Improving ROS-Scavenging Capability.

Late embryonic developmental abundant (LEA) genes play a crucial role in the response to abiotic stress and are important target genes for research on plant stress tolerance mechanisms. Acer truncatum Bunge is a promising candidate tree species for investigating the tolerance mechanism of woody plants against abiotic stress. In our previous study, AtruLEA1 was identified as being associated with seed drought tolerance. In this study, LEA1 was cloned from A. truncatum Bunge and functionally characterized. AtruLEA1 encodes an LEA protein and is located in the nucleus. Phylogenetic tree analysis revealed a recent affinity of the AtruLEA1 protein to AT3G15760.1. Overexpression of AtruLEA1 resulted in enhanced tolerance of Arabidopsis thaliana to drought and salt stress and heightened the ABA sensitivity. Compared to wild-type (WT) plants, plants with overexpressed AtruLEA1 exhibited increased activities of antioxidant enzymes under drought stress. Meanwhile, the ROS level of transgenic Arabidopsis was significantly less than that of the WT. Additionally, the stoma density and stoma openness of AtruLEA1 Arabidopsis were higher compared to those in the WT Arabidopsis under salt and drought stress conditions, which ensures that the biomass and relative water content of transgenic Arabidopsis are significantly better than those of the WT. These results indicated that AtruLEA1 was involved in salt and drought stress tolerances by maintaining ROS homeostasis, and its expression was positively regulated by abiotic stress. These results indicate a positive role of AtruLEA1 in drought and salt stress and provide theoretical evidence in the direction of cultivating resistant plants.

The GRAS transcription factor OsGRAS2 negatively impacts salt tolerance in rice.

Transcription factor OsGRAS2 regulates salt stress tolerance and yield in rice. Plant-specific GRAS transcription factors are involved in many different aspects of plant growth and development, as well as in biotic and abiotic stress responses, although whether and how they participate in salt stress tolerance in rice (Oryza sativa) remains unclear. A screen of a previously generated set of activation-tagged lines revealed that Activation Tagging Line 63 (AC63) displayed a salt stress-sensitive phenotype. Subsequent thermal asymmetric interlace polymerase chain reaction (TAIL-PCR) showed that AC63 was due to overexpression of OsGRAS2. Ectopic overexpression of OsGRAS2 caused increased salt stress sensitivity, while osgras2 loss-of-function lines displayed salt stress-resistant phenotypes. Further, we observed that OsGRAS2 impacts Na+ and K+ ion homeostasis in the shoots. Mutation of OsGRAS2 increased salt tolerance without yield penalty. Phylogenetic tree analysis indicated that OsGRAS2 belonged to the LISCL subfamily of GRAS transcription factors and had high amino acid similarity to OsGRAS23. Both OsGRAS2 and OsGRAS23 underwent homomeric and heteromeric interactions, indicating that they formed homo- and hetero-dimers. Moreover, OsGRAS2 and OsGRAS23 showed transcriptional activation activity that was mostly governed by motif1, which was located at the N-terminal region. Further, we found OsGRAS2 binds to the OsWRKY53 promoter to increase its expression, thereby negatively impacting the OsHKT1;5 expression. This study demonstrates a novel insight into how LISCL subfamily GRAS transcription factors impact salt stress tolerance in rice.

Molecular detection of Enterobacter hormaechei in bovine respiratory disease.

Bovine respiratory disease (BRD) develops from complex interactions among environmental, host and pathogenic factors. This study aimed to phenotypically identify Enterobacter hormaechei isolated from cattle with BRD and assess antimicrobial susceptibility and determining the molecular phylogeny of local E. hormaechei strains. Between November 2023 and March 2024, nasal swabs were collected from 93 cattle with BRD, before culturing for phenotypic analysis, and performing the polymerase chain reaction (PCR) for molecular characterisation. Of the 93 samples evaluated, 15.79% and 24.56% tested positive for E. hormaechei isolates on culture and PCR, respectively. The local isolates exhibited high resistance to amoxicillin, ampicillin, amikacin, nalidixic acid and ceftazidime; high susceptibility to azithromycin, levofloxacin, gentamicin, ofloxacin, cefepime, ceftriaxone, cefotaxime, nitrofurantoin, ceftazidime and ciprofloxacin; and moderate susceptibility to ciprofloxacin, colistin, imipenem and meropenem. Multiple sequence alignment, phylogenetic tree analysis and homology sequence identification, showed that the five positive isolates were similar to the reference isolate. To the best of our knowledge, this is the first time that E. hormaechei has been isolated in cattle with BRD in Iraq. Because phenotype-based assays show limited accuracy to identify species, we recommend molecular and phylogenetic analysis be included in all similar studies in the future.

DNA Barcoding Based on <i>matK </i>Gene and Phytochemistry Analyses of Local Balinese Kayu Tangi ( <i>Lagerstroemia</i> sp.)

Kayu tangi (Lagerstroemia sp.) is one of the medicinal plants that is often used traditionally by Balinese people for treating insomnia, diabetes, and dysentery. This study aims to determine the phylogenetic trees and the active compounds in Lagerstroemia tomentosa extract and its antioxidant activities. The methods used in molecular identification are DNA isolation, PCR, and DNA sequencing. The DNA sample was BLASTed to see its homology with the sequences in GenBank. These sequences were then used for phylogenetic tree analysis. The phytochemical analysis was done using the GC-MS method and the antioxidant activity test used the DPPH (1,1-diphenyl-2-picrylhydrazyl) after being reacted with the tested extract. The results of molecular identification showed that the samples used were closely related to Lagerstroemia tomentosa species (MW044208.1). The antioxidant activity test results showed an IC50 of 2.1 ugml-1 which is included in the very strong category. The phytochemical test results showed that the most dominant compounds contained in the plant stem bark were furfural (AUC 8.54%), beta-sitosterol (AUC 6.00%), and gamma-sitosterol (AUC 3.81%). Based on PubChem data, these compounds have antioxidant and antimicrobial properties as well as insecticide and herbicide. In conclusion, kayu tangi is very close to Lagerstroemia tomentosa and it’s potentially used as a medicine with strong antioxidant activities.

Prevalence and transmission of Salmonella collected from farming to egg processing of layer production chain in Jiangsu Province, China.

Salmonella is a common foodborne pathogen found in poultry production systems. Contaminated poultry products are a major source of human salmonellosis. Understanding the conditions of contamination and the genetic relationships of Salmonella in poultry production is necessary to develop effective interventions measures for controlling Salmonella transmission. Through epidemiological investigation and whole-genome sequence (WGS) analysis, this study revealed the epidemic law, drug resistance, and genetic characteristics of Salmonella in the production chain. In total, 130 (10.77 %) Salmonella strains were isolated from the collected samples, with Salmonella Enteritidis (S. Enteritidis) and S. Infantis being the predominant serotypes. WGS analysis revealed that the Sequence Type (ST) of all the 22 strains of S. Enteritidis were ST11, and 13 strains of S. Infantis were ST32. Antimicrobial resistance gene analysis showed that 95.45 % of S. Enteritidis carried strA/strB, sul, and blaTEM-1B; 77.3 % contained tetA genes; and 100 % of S. Infantis carried aac(6')-Iaa and mdf(A), which was consistent with the drug resistance phenotype. The phylogenetic tree showed that S. Enteritidis strains with different links were distributed in the same branch which displayed the very close genetic relationship. Combined with epidemiological investigations, it was found that S. Enteritidis infection begins at the chicken breeding stage and spreads vertically and horizontally along the production chain. In addition, phylogenetic tree analysis of S. Infantis showed that the genomes of 13 strains from egg products and egg collection center were very similar and belonged to the same clone cluster. It is speculated that the S. Infantis transmitted in the industrial chain is the same strain; it can spread along the industrial chain, and cross-contamination may occur. This study indicates that Salmonella contamination in the layered industrial chain is more serious and that a cloning relationship exists among the strains of different links. Therefore, more stringent measures should be taken to control Salmonella during the chicken breeding stage, and the importance of implementing good hygiene practices at every level of production should be emphasized.

First Report of Rust Caused by Cerotelium fici on Ficus carica L. in Korea.

Fig (Ficus carica L.) belonging to the Moraceae family is cultivated worldwide, with its primary production areas located in the Mediterranean region (Tous and Fergusen 1996). Yeongam-gun is a significant region for fig cultivation in Korea, accounting for 42% of the country's total fig cultivation area with approximately 1,400 fields (453ha, production yield 6000 tons). In July to November 2023, we observed severe rust disease in four fig orchards in Yeongam-gun (34°42'52.2"N, 126°31'32.16"E). The disease had affected 70% of the fig cultivation area (cv. Masui Dauphine). The area of each field is approximately 0.33~0.66ha, and 5 samples were collected from each field. Pustules of the pathogen were found in all samples. The diseased plants were deposited in the herbarium of the National Institute of Agricultural Sciences, Wanju, Korea (Specimen No. Cero_001). The initial symptoms were observed as chlorotic spots on the adaxial surface of the leaves, which developed into necrotic areas surrounded by chlorotic halos. Over time, dark brown spots were observed on the adaxial surface of the leaves, and abundant reddish-brown pustules were visible on the abaxial surface. Almost all leaves with these symptoms fell prematurely. Microscopic observation revealed that the urediniospores (n>50) were ellipsoidal, globose, obovoidal, or angular in shape, yellowish to faintly orange in color, sized 19.5-39.9 × 10.1-27.5 μm and had a wall thickness of 0.6-1.5 μm (average 1 μm). Telia were not observed. These morphological characteristics were comparable with that of Cerotelium fici (Gardner, 1997; Latinovic et al., 2015). For molecular analysis, genomic DNA was extracted from 3 to 5 samples, and the internal transcribed spacer region 2 (ITS2) and the large subunit (LSU) were amplified and sequenced using primer set: Rust2inv (Aime, 2006) and LR6 (Vilgalys and Hester, 1990). Furthermore, approximately 660 bp of the cytochrome c oxidase subunit III (COX3) gene was amplified and sequenced with CO3_F1 and CO3_R1 primers (Vialle et al., 2009). The obtained sequences were deposited in NCBI GenBank (GenBank accession no. PP491072 to PP491074 and PP491079 to PP491081). Phylogenetic tree analysis using the maximum likelihood method identified the isolate as Cerotelium fici. Pathogenicity test was conducted either by placing or by rubbing symptomatic leaf pieces on healthy leaves (5 leaves/plant) of three-year-olds fig plants (cv. Masui Dauphine) in a greenhouse in Wanju-gun, Jeonbuk special self-governing province. Healthy and symptom free leaf pieces were used for control. Two plants per treatment were used and the experiment repeated twice. The typical symptoms of fig rust disease were observed two weeks after inoculation in both methods. Control leaves were symptomless. C. fici was successfully reidentified from symptomatic tissues of inoculated leaves, fulfilling Koch's postulates and confirmed as a causal agent of fig rust. Fig rust caused by C. fici has been reported in New Zealand, Montenegro, Hawaii and other tropical regions (McKenzie, 1986). To our knowledge, this is the first report of fig rust in Korea caused by Cerotelium fici. It is believed that this will be helpful in research on the management of fig rust disease.

First Report of Powdery Mildew Caused by Erysiphe trifoliorum on Aeschynomene indica in China.

Aeschynomene indica is a semiaquatic legume that can be used as field green manure, forage grass, and medicinal plant (Zhang et al., 2019). It is also an "amphibious" plant commonly used as a wetland park green plant. In October 2020, typical powdery mildew symptoms were found on A. indica plants in Fanglan Lake Wetland Park, Jiujiang City, Jiangxi Province, China. More than 90% of A. indica plants were infected, and powdery mildew covered both sides of infected leaves, as well as stems and pods, forming circular to irregular patches. The infected leaves were collected to identify the pathogen, and microscopic examination revealed that there were abundant conidia and hyphae on the surface of the leaves. The conidia were solitary, elliptical to cylindrical, 23.23-38.03 μm in length and 9.14-17.56 μm in width (n = 100). The conidiophores were straight, cylindrical, unbranched, and ranged from 43.80 to 76.16 μm in length (n = 100). The foot cells were cylindrical or, rarely, somewhat curved at the base, 23.20-47.07 × 4.23-8.87μm (n = 100) and were followed by 1-2 shorter cells. Appressoria and chasmothecia were not observed on the collected samples. Based on these morphological characteristics, the powdery mildew fungus was tentatively identified as Erysiphe trifoliorum (Lee and Thuong, 2015). To further confirm this identification, the ribosomal DNA internal transcribed spacer (ITS) region and the partial sequence of the 28S large subunit (LSU) were amplified using primer pairs ITS1/ITS4 (White et al., 1990) and NL1/NLP2 (Mori et al., 2000), respectively. The obtained 662-bp ITS sequence (GenBank accession no. OK021589) was 99.55% identical to the ITS sequences of E. trifoliorumon Medicago littoralis in Azerbaijan (LC270860). The obtained 656-bp LSU sequence (GenBank accession no. PQ475931) was 99.69% identical to the ITS sequences of E. trifoliorumon Mimosa pudica in China (PQ184869). Additionally, a phylogenetic tree analysis was conducted based on the combined ITS and LSU sequences, which indicated that the isolate was grouped in the same clade as E. trifoliorum. Therefore, this fungus was identified as E. trifoliorum based on the morphological and molecular characteristics. Pathogenicity tests were performed by gently pressing infected leaves onto the young leaves of six healthy A. indica plants, and non-inoculated plants were used as controls. All plants were maintained in a greenhouse (25 ± 2 °C, 80% relative humidity, and a 16-hour photoperiod). After 14 days, typical powdery mildew features were observed on the inoculated plants, whereas no such features appeared on the control plants. The fungus on the inoculated leaves was morphologically and molecularly identical to that found on naturally infected plants collected from the Jiangxi Province. Powdery mildew caused by E. trifoliorum has been reported to affect some leguminous plants, including Indigofera amblyantha, Trifolium hybridum, Trifolium repens, and Melilotus indicus (Cho et al., 2016; Hong et al., 2020; Lee et al., 2015; Mukhtar et al., 2017). To our knowledge, this is the first report of powdery mildew caused by E. trifoliorum on A. indica in China, which seriously threatens the utilization of A. indica. The identification of E. trifoliorum as the causative agent of powdery mildew on A. indica is critical for the prevention and management of this disease in the future.

Tetraodon (Tetraodon nigroviridis) süperoksit dismutaz genlerinin (sod1, sod2 ve sod3) in siliko analizi ve dokuya özgü gen ekspresyon profili

The objective of this investigation was to conduct in silico analyses on superoxide dismutase (sod1, sod2, and sod3) genes in tetraodon (Tetraodon nigroviridis), employing bioinformatics tools, and to assess the gene expressions in various tissues such as the intestine, brain, kidney, liver, muscle, heart, eye, spleen, gills, stomach, ovary, and testis of tetraodon. To achieve this, tissue samples were obtained from both male and female tetraodon, spanning the aforementioned organs, with the purpose of acquiring cDNA. Total RNA was isolated from each tissue, and subsequently, the transcripts of sods genes were assessed using qPCR, while transcript quantities were determined through RT-qPCR. The in silico analyses encompassed the examination of gene structure, conserved gene synteny, phylogenetic tree analyses, and the identification of similarity-identity ratios with other vertebrates. When examining the transcriptional differences between male and female tissues for the Tetraodon sod1 gene, it was noted that, except for the heart tissue, all other tissues studied (including the liver, intestine, muscle, brain, eyes, spleen, gills, kidney, stomach, and gonads) exhibited significantly higher expression levels in male fish. Examining the results for the sod2 gene in male and female tetraodon, significant upregulation was observed in the liver, muscle, gills, intestine, ovary, and testis, with no statistical significance in tissues like the intestine, heart, and gonads. Regarding the sod3 gene in male and female tetraodon, heart, spleen, and stomach tissues did not show statistical significance, but the liver, intestine, gills, kidney, stomach, and gonads exhibited significantly higher expression in male fish (p<0.05).

Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing.

Based on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot (P. armeniaca) varieties were analyzed to provide a theoretical basis for revealing the phylogenetic relationship and classification of the common apricot. WGRS was performed on 53 common apricot varieties, and high-quality SNP sites were obtained after alignment with the "Yinxiangbai" apricot genome as a reference. Phylogenetic analysis, G matrix analysis, principal component analysis, and population structure analysis were performed using Genome-wide Complex Trait Analysis (GCTA), FastTree, Admixture, and other software. The average comparison ratio between the sequencing results and the reference genome was 97.66%. After strict screening, 88,332,238 high-quality SNP sites were finally obtained. Based on the statistical SNP variation type, it was found that LNLJX had the largest number of variations (3,951,322) and the lowest base transition/base transversion ratio (ts/tv = 1.77), indicating that its gene exchange events occurred less frequently. Based on the SNP point estimation of the relationship and genetic distance between samples, the relationship between species was 1.41-0.01, among which PLDJX and BK1 had the closest relationship of 1.41, and YZH and LGWSX had the farthest relationship of 0.01. The genetic distance between species was 0.00367-0.264344, the genetic distance between HMX and JM was the closest, and the genetic distance between WYX and YX was the farthest, which was the largest. Phylogenetic tree, PCA, and genetic structure analysis results all divided 53 common apricot varieties into four groups, and the classification results were consistent. The SNP markers mined using WGRS technology are useful not only to analyze the variation of common apricots, but also to effectively identify their kinship and genetic structure, which plays a critical role in the classification and utilization of common apricot germplasm resources.

Zoonotic Surveillance of Bartonella spp.: Exploring the Public Health Risks in Human Settlements.

Urban rodents are reservoirs of zoonotic pathogens, including Bartonella spp., which are transmitted by ectoparasites such as fleas. Zoonotic diseases caused by Bartonella often go undocumented due to confusing or subtle clinical symptoms, lack of awareness and poor diagnosis. This study aimed to assess the prevalence and diversity of Bartonella spp. by screening free-ranging rodents and their ectoparasites in the unique ecological settings of Alipore Railway Station, Kolkata, India. The station's high passenger traffic and proximity to food stalls create favourable conditions for rodents and fleas to thrive, increasing the risk of zoonotic transmission. Rodents and fleas were identified by morphological features and DNA sequencing. Detection of Bartonella was carried out by DNA sequencing of citrate synthase (gltA) gene. Phylogenetic relationships among the obtained sequences were inferred through phylogenetic tree and haplotype network analyses. Q-PCR testing from human samples from the surrounding area was performed to confirm the zoonotic transfer potential. Of 60 rodents, identified as Bandicota indica 28 (46.7%) and Bandicota bengalensis 32 (53.3%), and 110 fleas (Xenopsylla cheopis) were collected. The prevalence of Bartonella infection varied across three different hosts, that is, 32/60 rodents (53.33%), 87/110 fleas (79.1%) and 4/25 human (16%). Phylogenetic analysis revealed four distinct Bartonella lineages comprising 11 novel haplotypes (H1-H11), with haplotype H4 shared between rodents, fleas and humans, indicating active and cross species transmission of Bartonella spp. Haplotype H10, identified as B. rochalimae, was a phylogenetically diverged lineage exclusively found in fleas, suggesting a potentially novel lineage. The results highlight the significant public health risks posed by Bartonella spp. in densely populated urban areas, particularly in environments like railway stations where human-rodent interactions are frequent. This study underscores the necessity of integrated pest management and surveillance strategies, using molecular tools such as Q-PCR, to mitigate the risk of zoonotic disease transmission in urban settings.