Phylogenetic Tree Analysis Research Articles

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.

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).

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.

Genetic Analysis of the Peach SnRK1β3 Subunit and Its Function in Transgenic Tomato Plants

Background/Objectives: The sucrose non-fermentation-related kinase 1 (SnRK1) protein complex in plants plays an important role in energy metabolism, anabolism, growth, and stress resistance. SnRK1 is a heterotrimeric complex. The SnRK1 complex is mainly composed of α, β, βγ, and γ subunits. Studies on plant SnRK1 have primarily focused on the functional α subunit, with the β regulatory subunit remaining relatively unexplored. The present study aimed to elucidate the evolutionary relationship, structural prediction, and interaction with the core α subunit of peach SnRK1β3 (PpSnRK1) subunit. Methods: Bioinformatics analysis of PpSnRK1 was performed through software and website. We produced transgenic tomato plants overexpressing PpSnRK1 (OEPpSnRK1). Transcriptome analysis was performed on OEPpSnRK1 tomatoes. We mainly tested the growth index and drought resistance of transgenic tomato plants. Results: The results showed that PpSnRK1 has a 354 bp encoded protein sequence (cds), which is mainly located in the nucleus and cell membrane. Phylogenetic tree analysis showed that PpSnRK1β3 has similar domains to other woody plants. Transcriptome analysis of OEPpSnRK1β3 showed that PpSnRK1β3 is widely involved in biosynthetic and metabolic processes. Functional analyses of these transgenic plants revealed prolonged growth periods, enhanced growth potential, improved photosynthetic activity, and superior drought stress tolerance. Conclusions: The study findings provide insight into the function of the PpSnRK1 subunit and its potential role in regulating plant growth and drought responses. This comprehensive analysis of PpSnRK1 will contribute to further enhancing our understanding of the plant SnRK1 protein complex.

Genetic diversity and population structure analysis of 418 tomato cultivars based on single nucleotide polymorphism markers.

Tomato (Solanum lycopersicum) is a highly valuable fruit crop. However, due to the lack of scientific and accurate variety identification methods and unified national standards, production management is scattered and non-standard, resulting in mixed varieties. This poses considerable difficulties for the cataloging and preservation of germplasm resources as well as the identification, promotion, and application of new tomato varieties. To better understand the genetic diversity and population structure of representative tomato varieties, we collected 418 tomato varieties from the past 20 years and analyzed them using genome-wide single nucleotide polymorphism (SNP) markers. We initially assessed the population structure, genetic relationships, and genetic profiles of the 418 tomato germplasm resources utilizing simplified genome sequencing techniques. A total of 3,374,929 filtered SNPs were obtained and distributed across 12 chromosomes. Based on these SNP loci, the 418 tomatoes samples were divided into six subgroups. The population structure and genetic relationships among existing tomato germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Rigorous selection criteria identified 15 additional high-quality DNA fingerprints from 50 validated SNP loci, effectively enabling the identification of the 418 tomato varieties, which were successfully converted into KASP (Kompetitive Allele Specific PCR) markers. This study represents the first comprehensive investigation assessing the diversity and population structure of a large collection of tomato varieties. Overall, it marks a considerable advancement in understanding the genetic makeup of tomato populations. The results broadened our understanding of the diversity, phylogeny, and population structure of tomato germplasm resources. Furthermore, this study provides a scientific basis and reference data for future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding in tomatoes.

Genome-wide identification of gap junction gene family and their expression profiles under low temperature stress in noble scallop Chlamys nobilis

Gap junctions, formed by gap junction proteins (GJ), play crucial roles in cell signaling and immune responses. The structure and function of the GJ from vertebrates (called connexins) have been extensively studied. However, little is known about the proteins forming gap junctions in invertebrates (called innexins). In this study, 14 GJ genes of Chlamys nobilis were identified. GJ proteins are mainly distributed on the plasma membrane, and all proteins are hydrophilic Phylogenetic tree analysis showed that the GJ proteins in C. nobilis were distantly related to those in vertebrates but closely related to those in invertebrates. Conserved motifs analysis of these GJ proteins in C. nobilis identified to have 10 conserved motifs, similar to gap junction proteins in other bivalves. Moreover, expression profiles of CnGJ genes under chronic and acute low temperature stress were also investigated. Results showed that chronic low temperature stress had a significant effect on the expression levels of CnGJ genes, and the expression profiles of CnGJ genes showed significantly variation under acute low temperature stress. All these results indicated that CnGJ genes play important roles in environmental adaptation in scallops. The present study initially elucidated the function of gap junction genes in noble scallop C. nobilis, which provides new insights into the GJ genes in mollusks and will help us better understand their roles in environmental stress in scallops.

Genome-wide identification of SWEET gene family and the sugar transport function of three candidate genes during female flower bud induction stage of Juglans sigillata Dode

Sugar Will Eventually be Exported Transporter (SWEET) transports sugar to sink organs and regulates intercellular sugar transport to provide energy for plant growth and development. In this study, twenty-two SWEET genes were identified and distributed on eleven chromosomes. Phylogenetic tree analysis showed that these genes could be divided into four subfamilies. Metabolism and transcriptome analysis showed that sucrose and fructose were accumulated in female flower buds at physiological differentiation stage (PDS). The third branch of JsSWEET1 and the fourth branch of JsSWEET9 and JsSWEET17 were highly expressed in female flower buds at undifferentiated stage (UDS) and PDS, which promoted sugar accumulation in female flower bud differentiation, so these three candidate SWEET genes were considered to be involved in the accumulation of sugar in the flower bud differentiation of Juglans sigillata. The subcellular localization showed that all three candidate genes were located on the cell membrane, and JsSWEET17 was also expressed and functioned in the vacuolar membrane. Through overexpression in callus and silencing in female flower buds at UDS and PDS, it was found that JsSWEET1 positively regulated the accumulation of sucrose in female flower buds, and JsSWEET9 and JsSWEET17 are involved in the transport and accumulation of fructose during flower bud differentiation. These results could provide a comprehensive understanding of the JsSWEETs gene family and provide theoretical guidance for further study of the function of SWEET-induced sugar accumulation in plant flower development.

Pometia pinnata (J.R.Forst. & G.Forst.) as urban tree species: A chloroplast genome and phylogenetic studies

Abstract Pometia pinnata (J.R.Forst. & G.Forst.) is a native Indonesian forest plant increasingly used in urban landscaping. It produces both edible fruits and valuable timber. As with other tree species, enhancing its genetic quality is essential to maximize the utilization of this promising species. However, the information on genetic and genomic data is still lacking, including the analysis of the genetic relationship of this species. This study aims to generate the chloroplast genome of P. pinnata, identify the most suitable DNA marker, and evaluate the relationship within the Sapindaceae family using long-read sequence data generated by MinION Oxford Nanopore Technologies (ONT). The study involved several steps: DNA extraction, DNA quality and quantity tests, DNA sequencing, assembly of the chloroplast genome, and reconstruction of a phylogenetic tree using three markers, i.e., rbcL, matK, and rbcL+matK combinations. The DNA sequencing yielded 449,068 reads, with 2,856 reads after mapping, an N50 read length of 4,188 bp, a total base of 1,135,927 Mb, and a chloroplast genome of 160,372 bp. These results indicated that the DNA isolated from P. pinnata is good quality. Phylogenetic tree analysis revealed that the combination of rbcL and matK markers effectively differentiates groups within the Sapindaceae family, revealing P. pinnata as closely related to Nephelium lappaceum, Nephelium mutabile, Sapindus mukorossi, Dimocarpus longan, Bligia sapida, Litchi chinensis, Acer yangbiense, and Lepisanthes alata. This study enriches genetic studies on P. pinnata, establishing a foundation for species identification based on the rbcL and matK marker and supporting future tree improvement programs.

Molecular characterization of human respiratory syncytial virus strains circulating among hospitalized children in Jordan

BackgroundHuman Respiratory Syncytial Virus (HRSV) is a primary cause of severe pediatric respiratory infections, particularly in infants and young children, often resulting in hospitalization. The virus possesses a high degree of mutagenic potential, contributing to significant antigenic diversity, which complicates immune responses and poses challenges for vaccine development and disease management. This study was conducted in Jordan from 2022 to 2023 to epidemiologically determine the prevalence and molecular characteristics of RSV.MethodsA total of 288 nasopharyngeal (NP) swabs were collected from hospitalized children at Prince Hamza Hospital, Amman, Jordan. All samples were screened for common viral and bacterial respiratory pathogens using PCR. A partial segment of the G gene of RSV was amplified for molecular characterization and phylogenetic tree analysis.ResultsViral and/or bacterial infection was identified in 71.9% (207/288) of the tested specimens. Among these, 35 samples (12.2%, 35/288) tested positive for RSV. Specific subgroup PCR analysis identified (25, 71.4%) RSV-A, (4, 11.4%) RSV-B, and (6, 17.1%) could not be identified using our set of primers. Phylogenetic tree analysis revealed that RSV-A ON1 and RSV-B BA9 genotype strains predominate in Jordan. We observed multiple substitutions in our studied sample which would drive variation in the level of antigenicity and pathogenicity of RSV. Glycosylation sites identified were consistent with previously reported studies.ConclusionThis study provides updated epidemiological data on the strains circulating in Amman, Jordan and their molecular characteristics. Continuous RSV surveillance informs vaccine development, guides public health interventions, and enables timely administration of prophylactic treatments, reducing the burden of RSV-related illness.

Screening of SNP Loci Related to Leg Length Trait in Leizhou Goats Based on Whole-Genome Resequencing.

Leizhou goats can be classified into tall and short types based on their size and habits. The tall Leizhou goats are well-suited for grazing management due to their robust physique, while the dwarf types are smaller, grow rapidly, and are more appropriate for feeding management systems. In this study, whole-genome resequencing was conducted to identify genomic variants in 15 Tall-legged (TL) and 15 Short-legged (SL) Leizhou goats, yielding 8,641,229 high-quality SNPs in the Leizhou goat genome. Phylogenetic tree and principal component analyses revealed obvious genetic differentiation between the two groups. Fst and θπ analyses identified 420 genes in the TL group and 804 genes in the SL group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the phosphatidylinositol signaling system is associated with growth and development. Additionally, Genome-Wide Association Study (GWAS) analysis identified eight genes linked to leg length, including B4GALT7 and NR1D1. Notably, the NC_030818.1 (g.53666634T > C) variant was significantly associated with leg length traits, where the CC genotype was linked to shorter legs and the TT genotype to longer legs. This study identifies candidate genes and molecular markers, serving as a reference point for breeding and genetic improvement efforts in Leizhou goats and other goat breeds.

Characterization of Pseudomonas aeruginosa Isolated from Bovine Mastitis in Northern Jiangsu Province and Correlation to Drug Resistance and Biofilm Formability.

This study aimed to provide experimental support for the prevention and treatment of Pseudomonas aeruginosa infections and to elucidate the epidemiological distribution of resistance and virulence genes of Pseudomonas aeruginosa from mastitis in dairy cows in the northern part of Jiangsu Province and their relationship with the biofilm-forming ability of the strains. Mastitis presents a significant challenge within dairy farming, adversely impacting the health of dairy cows and precipitating substantial economic losses in milk production. In this study, Pseudomonas aeruginosa (PA) was isolated and identified from mastitis milk samples in Jiangsu Province, China. In order to characterize the isolates, multilocus sequence typing (MLST), drug resistance phenotypes, virulence genes, and biofilm formations were detected. The isolation and identification of pathogenic bacteria from 168 clinical mastitis milk samples using 16S rRNA and PCR revealed 63 strains of Pseudomonas aeruginosa, which were determined to be highly homologous according to phylogenetic tree analysis. In addition, the MLST indicated five major ST types, namely ST277, ST450, ST571, ST641, and ST463. The susceptibility to 10 antimicrobials was determined, and it was found that 63 strains of Pseudomonas aeruginosa did not have a strong resistance to the antimicrobials in general. However, there were differences in the phenotypes' resistance to antimicrobials among the different ST types. It was also found that the more resistant the strains were to antimicrobials, the lower the carriage of virulence genes detected. The biofilm content was measured using the semi-quantitative crystal violet method. It was found that there were a few strains with medium or strong biofilm-forming abilities. However, the number of virulence genes carried by the 63 strains of Pseudomonas aeruginosa was inversely proportional to the biofilm-forming ability. It was also found that there were significantly more Pseudomonas aeruginosa in the biofilm state than in the planktonic state and that strains with strong biofilm-forming abilities were more resistant to antimicrobials.

Complete chloroplast genomes of three Polygala species and indel marker development for identification of authentic polygalae radix (Polygala tenuifolia).

In Korea, only Polygala tenuifolia is registered as Polygalae Radix in the pharmacopoeia, while in China, both P. tenuifolia and P. sibirica are used equally. Accurate identification of herbal medicines is crucial for their safety and efficacy, but commercial products are typically sold in dried form, making morphological distinction difficult. Therefore, a quick and accurate method to distinguish P. tenuifolia is necessary for proper utilization of medicinal herb. We aimed to identify specific molecular markers for P. tenuifolia to avoid confusion regarding its pharmacological efficacy and to evaluate the classification of Polygala using plastid phylogenetic data. We analyzed the sequences of three species distributed in Korea, P. tenuifolia, P. japonica, and P. sibirica, and assembled their chloroplast genome sequences. Comparative analysis revealed regions of local divergence, and six molecular markers were developed from these hotspots. Additionally, a phylogenetic tree was constructed to determine the phylogenetic positions of the three Polygala species. The marker successfully identified the three Polygala species, and all commercial products and breeding lines tested were confirmed to be P. tenuifolia and recognized as authentic. Phylogenetic analysis revealed that P. tenuifolia forms a distinct cluster from P. sibirica and P. japonica. We determined the chloroplast genomes of the three Polygala species and performed phylogenetic tree analysis and marker development. Indel markers were developed to identify the critical herbal species, P. tenuifolia. This comprehensive study of the Polygala chloroplast genome provides useful information for P. tenuifolia identification.

First report of Rhizoctonia solani AG-2-2 IIIB causing Rice sheath blight in China.

Rice (Oryza sativa) is an important crop worldwide, rice is susceptible to many pathogens, one of the most significant being Rice Sheath Blight, caused by Rhizoctonia solani. This disease initially produces cloudy spots on the leaf sheaths and later affects grain filling, resulting in yield losses of over 45%（Chen et al. 2013） when severe. In many southern rice-growing areas of China, the impact of this disease has risen to become the most damaging of the three major rice diseases (Margani et al. 2018). In July 2023, In Yongfu County, Guangxi (110.022°E, 25.010°N), symptoms of rice sheath blight were observed. The leaf sheaths were affected, with small, water-soaked, dark green spots with indistinct edges appearing near the water surface. These spots gradually expanded into elliptical or cloud-like lesions. Eventually, the center of the lesions turned straw-yellow to grayish-white, while the edges turned brown to dark brown. Often, several lesions merged into large cloud-like patches. Fifteen symptomatic sheaths were collected disinfecting pieces of necrotic tissue with 3% NaClO for 1.5 minutes, followed by 75% alcohol for 1 minute. The pieces were then rinsed with sterile distilled water, subsequently plated on Potato Dextrose Agar in Petri dishes, and incubated at 28°C in the dark. One isolate was obtained from each diseased plant using the hyphal tip method. (Feng et al. 2008). Isolates were obtained and displayed initially white mycelium and gradually turned brown after three to four days. Septate hyphae were 4.27 to 10.73 μ m (average 6.41 μ m) in diameter and branched at Right angle or acute angle with a constriction at the origin of the branch point. Staining with 1% safranin O and 3% KOH solution (Bandoni 1979) revealed multinucleated cells (three to nine nuclei per cell, n = 144). In summary, these characteristics were consistent with the description of Rhizoctonia solani Kühn (Meyer et al. 1990). The anastomosis group (AG) was confirmed by selecting three representative isolates (GL-Q-10, GL-Q-13, GL-Q-15) for molecular identification. The target DNA was extracted using Chelex-100. The internal transcribed spacer (ITS) region was amplified and sequenced with primers ITS1 and ITS4. The sequences were deposited in GenBank (ITS, PQ047154, PQ047150, and PQ047151 The base pairs are respectively 713bp, 715bp and 776bp, respectively). Upon searching GenBank, accession number MT385836 was found (Zhou et al. 2021), which has a similarity of 99.15% with PQ047154, 98.87% with PQ047150, and 99.30% with PQ047151. Phylogenetic tree analysis based on ITS sequences showed that the isolates clustered monophyletically with strains of R. solani AG-2-2 IIIB. The fusion group of the strain is verified by the shape and color of its mycelial growth on PDA at 35°C, enabling the distinct differentiation of AG-2-2 IIIB from AG-2-2 IV in terms of both morphology and coloration.（Aktaruzzaman et al. 2019） Pathogenicity tests involved culturing the pathogenic bacteria on PDA for 7-10 days, Then, 10 healthy rice plants (greenhouse potted rice variety Dian Heyou 615) were selected at the heading stage, and 5 plants were inoculated on the leaf sheaths with 5 strains of 5 mm fungus cake with pathogenic bacteria and 5 plants without pathogenic bacteria (The rice soil was disinfected), wrapped in cotton for moisture retention. All plants were sealed in transparent plastic bags and incubated in a greenhouse at 30 °C for 7-15 days, with daily moisturizing using sterile distilled water (Humidity control at 70%). Seven days postinoculation, Those containing pathogenic bacteria have symptoms of rice sheath blight, No symptoms were detected on control plants. Rhizoctonia solani AG-2-2 IIIB was re-isolated from the inoculated plants as previously described, thus fulfilling Koch's postulates. The pathogenicity tests were repeated three times. At present, Rhizoctonia solani AG-2-2 IIIB is primarily pathogenic in plants such as sugar beet and beans. It has only been reported in Japan and other countries to cause rice disease (Engelkes et al. 1996; Kenji Inagaki et al. 2004), and Rhizoctonia solani AG-2-2 IIIB has never been reported in China to cause disease in rice. To our knowledge, this study is the first to identify Rhizoctonia solani AG-2-2 IIIB causing rice sheath blight in China. This finding will aid further research on rice sheath blight defense strategies and contribute to the development of better management practices for this disease.

Transcriptome and genome-wide analysis of the mango glycosyltransferase family involved in mangiferin biosynthesis

Mangiferin, a C-glucosyl xanthone, is a biologically active glycoside naturally synthesized in mango. Glycosyltransferase can catalyze the biosynthesis of mangiferin. In this study, we identified 221 members of the UGT glycosyltransferase family in mango. The 221 MiUGT genes were grouped into 13 subfamilies through phylogenetic tree analysis with Arabidopsis, Chinese bayberry, and mango. All UGT family members in mango were unevenly distributed on 17 chromosomes and found that tandem duplication dominated the expansion of UGT family members in mango. Purification selection primarily influenced the evolution of the mango UGT family members. In addition, cis-element analysis of the mango UGT gene family revealed the presence of MYB binding sites, which are involved in flavonoid biosynthesis; which further supports the role of UGT family members in the synthesis of flavonoids. To verify these results, we analyzed the expression of UGT family members in mango leaves, stems, and different developmental stages of fruit peel. The RNA-seq and qRT-PCR results showed significant differences in the expression patterns of MiUGT genes in various tissues and developmental stages of mango. We identified MiUGT gene-specific expression at different stages of fruit development. These results lay a theoretical foundation for research on the relationship between members of the mango UGT family and the synthesis of flavonoids, mangiferin.

Etiological characteristics of Brucella melitensis in Henan Province, 2013-2022

Objective: To analyze the genus, drug resistance/virulence and phylogenetic characteristics of Brucella strains isolated from brucellosis surveillance sentinels in Henan Province from 2013 to 2022, and provide baseline data for the surveillance, early warning and outbreak tracing of brucellosis. Methods: Blood samples were collected from patients with Brucella infection for strain isolation, culture and species identification, drug susceptibility test, whole genome sequencing, splicing and assembly, functional/virulence/resistance gene prediction analysis and phylogenetic tree drawing based on single nucleotide polymorphism (SNP). Results: In 36 brucellosis patients, the majority were men (86.11%, 31/36), young adults aged 18-50 (88.89%, 32/36) and farmers/herdsmen (72.22%, 26/36). A total of 36 strains of Brucella melitensis were isolated, and average 1 305 functional proteins of 21 categories were predicted by strain genome; all the strains carried four main virulence factors (pmm, VirB group, BtpA/BtpB, BvrS/BvrR). The drug sensitivity rate was 100.00% to six types of antibiotics including levofloxacin, rifampicin, doxycycline, streptomycin, tetracycline and gentamicin, they showed different resistances to three antibiotics including compound trimethoprim-sulfamethoxazole, ciprofloxacin and ampicillin. The strains carried four types of resistance genes and two clusters of resistance genes, with four combinations of genotypes, the resistance mechanisms included antibiotic degradation/modification enzymes, resistant nodular cell differentiation (RND) efflux pumps, 16S/23S ribosomal rRNA binding site mutations, etc. The number of SNP differed in the genomes of 36 Brucella melitensis strains ranged from 0 to 454 and phylogenetic tree was divided into three major branches, with relative branch distances between 0.000 0 and 0.498 6 for each strain. Conclusions: Human Brucella melitensis strains isolated from surveillance sentinels in Henan from 2013 to 2022 carried multiple virulence and antibiotic resistance genes and had different drug resistance phenotypes. Single nucleotide polymorphism analysis and phylogenetic tree analysis showed significant differences in phylogenetic relationships among different strains.

First Report of Lelliottia amnigena Causing Soft Rot on Purple Stem Mustards in China.

The purple stem mustards (Brassica rapa subsp. chinensis var. purpuraria) (Govaerts R, 2003) are widely cultivated along Yangtze River Valley in China, which is famous for its flavorful and nutritious edible stalks (Wang et al., 2022). In February 2023, a disease of soft rot was observed in multiple purple stem mustards planting fields in Wuhan city, Hubei province, China (30.41°N, 114.22°E). Disease incidence rates were almost 20 to 30% in the planting area (5 ha in size), causing severe economic loss. Infected plants displayed water-soaked symptoms at the base of the petioles, emitting a foul soft rot odor. The severely infected petioles, stems and roots exhibit pus symptoms leading to plant death. To identify the causal agent, small pieces of soft rot symptomatic tissue were cut from the margin of necrotic lesions and surface disinfected with 75% (v/v) ethanol for 30 seconds, followed by three successive rinses with sterile distilled water. The exudates from the clipped tissues were serially diluted and then incubated onto nutrient agar (NA) plates to obtain purified strains at 28°C for 48 hours (Koike et al., 2002). After incubation, 15 strains were obtained and the colonies of all strains were Gram-negative, aerobic, small, round, convex, whitish to dull white, and had smooth slimy edges. Three single bacterial strains CT020801 - CT020803, which were individually isolated from three different diseased samples, were selected as representative strains for further study. Biochemical tests using the BIOLOG GENIII microplate system (Biolog, Hayward, CA, USA) revealed that these strains were positive for methyl red, pectin, dextrin, D-Cellobiose, β-galactosidase, citrate, and maltose, but negative for indole, arginine dihydrolase, urease, ornithine decarboxylase, and gelatinase tests. The 16S ribosomal RNA gene and the three housekeeping genes, atpD, rpoB, and recN were amplified using genomic DNA of Lelliottia amnigena NCTC12124T as the template, with specially designed primers. All amplified fragments were sequenced and deposited in GenBank with accession numbers OQ954706-OQ954707, OQ954713, and OQ953873-OQ953881. BLAST alignments of the 16S rRNA, atpD, rpoB and recN sequences revealed that the sequences of Strain CT020801-03 exhibited the highest identity (100%, ≥97.97%, ≥98.85% and ≥94.52%, respectively) with L. amnigena （Figure S2）. Phylogenetic tree analysis based on multilocus sequence joint 16S rRNA - atpD - rpoB - recN revealed that CT020801 - CT020803 and L. amnigena clustered together in the same clade (Carrie et al., 2013). These results were consistent with those reported for Lelliottia amnigena (Osei et al., 2022). To confirm pathogenicity, healthy base petioles of three-week-old purple stem mustards seedlings were stab inoculated with 20 μL bacterial suspensions (approximately 108 CFU/mL) and then incubated at 28°C and 80% relative humidity in a growth chamber. A sterile liquid NB medium served as the negative control. The test was repeated thrice with each test consisting of five seedlings per treatment. After three days, soft rot symptoms appeared on the stem bases of the inoculated plants, consistent with the initial symptoms observed in the field. Control plants showed no symptoms. The strains were successfully re-isolated from symptomatic plants and identified as L. amnigena, fulfilling Koch's postulates. L. amnigena, a member of the Enterobacter genus (Birlutiu et al., 2023; Brady et al., 2013; Izard et al., 1981), is commonly found in soil and has been identified as an opportunistic pathogen responsible for plant soft rot disease (Reyes-García et al., 2020; Schroeder et al., 2009; Wu et al., 2023). Previous studies have linked L. amnigena to soft rot disease in potato tubers in China. However, this study marks the first documented case of L. amnigena causing soft rot disease in purple stem mustards in China. This discovery expands the known host range of the pathogenic bacteria and will help to provide essential information for making effective measures to manage this disease.

Estimating the Current Routes of Transmission in HIV-1 F1 Subtype Infected Persons in Romania: Differences Between Self-Reporting and Phylogenetic Data.

Monitoring the HIV epidemic in Romania has proven challenging due to many factors, including the reluctance of newly diagnosed patients to disclose relevant epidemiological aspects during the clinical interview, such as sexual orientation or the existence of previous issues with injectable drug usage. We propose in this study a molecular approach to mitigate this problem with the help of bioinformatic tools, such as cluster analysis of phylogenetic trees. Both a maximum likelihood estimation, as implemented with FastTree, and a Bayesian approach, as used in BEAST, have been applied to our data set of 312 HIV subtype F1 pol gene sequences. ClusterPicker was used in order to identify groups of sequences and indicate similarities possibly related to the route of transmission. An important observation from this analysis is that transmission between men who have sex with men (MSM) is likely occurring in networks significantly larger than previously assessed by self-reported data (65% from the phylogenetic tree versus 37% from self-declared affiliation). Cluster analysis can help identify risk factors, reveal transmission trends, and, consequently, advise prevention programs.

Genomic analysis and characterization of lytic bacteriophages that target antimicrobial resistant Escherichia coli in Addis Ababa, Ethiopia

The emergence of antibiotic resistance in E. coli strains has sparked a fervent investigation of alternative therapies, such as the use of lytic bacteriophages. Phage genome sequence analysis is a novel method for learning more about proteins and other biomolecules encoded by phages, particularly phage-lytic enzymes that are crucial to the lysis of bacterial cells. Seven potential lytic E. coli phages—EH-B-A (A1), EP-M-A, EP-B-K (E2), EI-SP-GF, ET-SD-TH, and ST-TK—isolated from activated dairy farm sludges, rivers, and hospital liquid waste genomes were described in this study. The Illumina NextSeq 550 sequencer was used for sequencing phage isolates. The virus nucleotide collection (nr/nt) (taxid:10239) was used to evaluate whole-genome sequences. Phylogenetic analysis was performed using the MEGA11 software. Genome sequencing revealed that each bacteriophage contained a linear double-stranded DNA genome. Phage isolates were taxonomically identified as the Caudoviricetes class with four genera of phages, including Kagunavirus, Vequintavirus, Dhillonvirus, and Jilinvirus. Phage genome lengths varied from 24,264 to 136,204 bp, and GC contents ranged from 44 % to 55 %. In total, 33–218 CDSs (coding sequences) were predicted, with 19–77 % of CDSs encoding functional proteins. All phages lacked tRNA genes in their genomes, except for EI-SP-GF, which possessed five tRNA genes. Based on the phylogenetic tree analysis, the phage isolates were related to Enterobacteria and E. coli phage sequences in the database. Screening did not show any genes encoding for a CRISPR-like system, virulence, antibiotic resistance, or lysogeny. Because of their stringent lytic nature, these phage isolates might be used in the future to treat E. coli infections. This study might also provide some primary data for developing phage control techniques and advance our understanding of the genetic composition of E. coli phages.

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.

The antibacterial defence role of β-defensin in the seahorse testis

Seahorses represent the only known group of animals with male pregnancy. Seahorses have small testis that produce a limited quantity of sperm. To date, the response of this immune-privileged organ to pathogenic infections has not been reported. β-defensin (BD) is an important innate immune defence factor against pathogens in vertebrate testis. To elucidate its immunoprotection in seahorse testis, we identified the Hippocampus erectus β-defensin (HeBD) sequence in its genome via phylogenetic tree and protein-sequence structure analysis. Gene-expression analysis showed that HeBD was highly expressed in the seahorse testis and was significantly upregulated after bacterial infection, indicating that HeBD expression was related to testicular immune responses. Furthermore, antibacterial activity testing demonstrated that the mature HeBD peptide exhibited broad-spectrum aggregation activity but only moderate antibacterial activity. We found that the mature HeBD mature significantly neutralised bacterial endotoxin activity. In conclusion, our results imply that HeBD serves an immunoprotective role in seahorse testis.