NCBI GenBank Research Articles

Biodegradation of Imidacloprid by the Local Isolate Rhizobium pusense

Imidacloprid is systemic insecticide (1-[(6-chloro-3-pyridinyl) methyl]-N-nitro-2-imidazolidinimine) and the world’s most widely used has significant efficacy against a broad variety of pests and a unique mode of action by using it spreader and irrigation. The persistence of this pesticide in the soil means that it causes environmental damage that must be cleaned up. In this study collected and identified the best bacteria isolate that breakdown imidacloprid from the Plant Protection Director in Baghdad, which has been using neonicotinoid pesticides for years in their own greenhouse for pest control. Using high-performance liquid chromatography HPLC to measuring the residual concentrations of imidacloprid in MSM media at a concentration of 25 mg/L for 21 days to know the best degrading bacterial isolate for imidacloprid. The best bacterial isolate No.43 was able to degrade 50.2% for 21 days of imidacloprid which was identified as Rhizobium pusense according to morphological, cultural and biochemical tests. Moreover, genetic analysis for the 16S rRNA gene and given a new accession number (OP218458.1.) in the GenBank of NCBI. It could be concluded, from this study that the soil previously contaminated for long periods of time with imidacloprid can be treated by degrading the imidacloprid residues in it by isolated bacteria Rhizobium pusense.

Bioremediation of Imidacloprid by the Local Isolate Psychrobacter celer

Pesticide biodegradation can be accomplished by the technique of bioremediation, which makes use of microorganisms’ ability to degrade pesticide residues. This study aimed to separate and identify imidacloprid-biodegradable from botanical fields soil of greenhouses in the Plant Protection Directorate /Ministry of Agriculture in Baghdad, which has been using imidacloprid pesticides for many years. Using high-performance liquid chromatography, residual imidacloprid concentrations in MSM medium at a concentration of 25 mg/L after 21 days were measured to identify the best degrading bacterial isolates. Isolate No.37 the best bacterial isolate was able to degrade 63% of imidacloprid. was identified as Psychrobacter celer according to morphological, cultural and biochemical tests. Moreover, genetic analysis for the 16S rRNA gene and given a new accession number (OP672320.1) in the GenBank of NCBI, from this study that the soil previously contaminated for long periods of time with imidacloprid can be treated by degrading the imidacloprid residues in it by isolated bacteria Psychrobacter celer.

First report of Zymoseptoria tritici causing Septoria tritici blotch in wheat in Paraguay.

Wheat (Triticum aestivum) is the third most cultivated field crop in Paraguay; it is grown on over 450,000 hectares with an annual production of 927,776 tons (fao.org/faostat). In 1952, Septoria tritici blotch (STB) was associated with the fungus Septoria tritici solely based on microscopic observation of conidia (Viedma and Delgado 1987). However, no morphometric or molecular studies have been performed in Paraguay up to date. Over the following decades, STB epidemic outbreaks were recorded, with a reduction in wheat production of up to 70% (Viedma and Delgado 1987). During winter 2021, leaf blotch symptoms were observed with an incidence above 50% in wheat fields in Capitán Miranda, Itapúa, Paraguay. Scattered, spherical, buried, and light brown necrotic spots with dark edges were observed on the leaves. Pycnidia with prominent central ostiole were observed. Leaves with symptoms were washed with 1% sodium hypochlorite for 1 min, rinsed with sterile distilled water, and incubated in wet chambers to induce sporulation of the fungus. Pycnidia produced greyish to white cirri. Isolated conidia were thin, elongated, and hyaline, ranging from 26.9-72.7 × 1.5-2.9 μm with one to three septa. Monosporic colonies on potato dextrose agar (PDA, ; Difco laboratories, Detroit, MI) media varied in color from white to pink, dark gray to black, or black with stroma-like structures. Based on morphology, the fungus was characterized as Zymoseptoria tritici (Hoorne et al. 2002; Gilchrist-Saavedra et al. 2005). Fungal DNA was extracted from mycelia, and the internal transcribed spacer (ITS), translation elongation factor 1-α (TEF1-α), 28S rRNA gene (LSU), actin gene (act), calmodulin (CaM) were amplified using ITS1/ITS4, EF1-728F/EF-2, LSU1Fd/ LR5, ACT-512F/ACT-783R, CAL-228F/CAL737R primers, respectively. PCR amplicons were sequenced at Macrogen (Seoul, Republic of Korea) and deposited in the NCBI GenBank database (ITS: OQ360718; TEF1-α: OQ999044, LSU: OQ996413, act: OQ999046, CaM: OQ999045). Sequences were aligned with several isolates of Septoria spp. previously reported (Verkley et al. 2013; Stukenbrock et al. 2012) using ClustalW. The alignments were concatenated with Bioedit (Hall 1999). The UPGMA method with 1,000 bootstrap replications, was used to construct the phylogenetic tree using MEGA11 with Readeriella mirabilis as the outgroup. The isolate from Paraguay grouped into the Zymoseptoria tritici clade with 96% bootstrap support. To confirm pathogenicity, ten wheat plants cv. Itapúa 80 were grown in pots for three weeks in growth chambers (22 ± 2°C; 16 h photoperiod). Subsequently, these plants were inoculated with 1×107 conidia ml-1 suspension, and ten non-inoculated plants served as control. Seven days after inoculation (DAI), symptoms were observed displaying oval necrotic lesions and approximately 14 DAI abundant pycnidia were observed on and around the lesions. Segments of symptomatic leaves were placed in moisture chambers overnight to enhance cirri development. Conidia were mounted on a slide and observed under the compound microscope. Individual cirrhus were transferred to plates containing PDA and produced colonies like those used in the inoculation (Hoorne et al. 2002). We confirmed that the causal agent of STB from wheat fields in Paraguay was Zymoseptoria tritici. This pathogen causes annual wheat disease epidemics in Paraguay; therefore, optimizing surveillance for early detection and understanding its distribution will improve integrated management.

Analysis of Antiphage Systems in Vibrio Cholerae O1 El Tor Biotype Strains

Introduction: Cholera lytic phages contribute to the genetic diversity and evolution of Vibrio cholerae. To protect against the phages, the pathogen has acquired various resistance mechanisms. Objective: To identify antiphage systems located on mobile genetic elements in V. cholerae serogroup O1 El Tor biotype strains. Materials and methods: Nucleotide sequences of complete genomes of 77 toxigenic V. cholerae O1 El Tor strains imported to the Russian Federation and neighboring countries in 1970–2014 were analyzed using the Blast NCBI GenBank algorithm and REALPHY online tool. Results: We observed that the examined strains contained two types of anti-phage systems in hotspot 5 of the ICE SXT element: BREX, common for ICE VchBan9, and BREX with Abi typical of ICE VchInd5. We established a direct relationship between the presence of the PLE4 antiphage island and the kappa phage. V. cholerae O1 El Tor strains containing PLE4, except for one isolate, have BREX ICE VchBan9 and are grouped into a separate cluster in phylogenetic analysis. Strains with ICE VchInd5 lacking PLE4 and kappa phage also form a separate group. Conclusions: The data obtained on the presence of antiphage systems in previously imported strains of V. cholerae O1 biotype El Tor expand knowledge of their genetic organization. The study of the structure of antiphage genes of hotspot 5 of the ICE SXT element makes it possible to reveal genetic differences between closely related strains of V. cholerae O1 biotype El Tor and to determine the type of ICE SXT element.

Barcoding and traditional health practitioner perspectives are informative to monitor and conserve frogs and reptiles traded for traditional medicine in urban South Africa.

Previous literature suggests that Indigenous cultural practices, specifically traditional medicine, are commonplace among urban communities contrary to the general conception that such practices are restricted to rural societies. We reviewed previous literature for records of herptiles (frog and reptile species) sold by traditional health practitioners in urban South Africa, then used visual confirmation surveys, DNA barcoding and folk taxonomy to identify the herptile species that were on sale. Additionally, we interviewed 11 IsiZulu and SePedi speaking traditional health practitioners to document details of the collection and pricing of herptile specimens along with the practitioners' views of current conservation measures for traditional medicine markets. The 34 herptile species recorded in previous literature on traditional medicine markets included endangered and non-native species. Spectrophotometry measurements of the DNA we extracted from the tissue of herptiles used in traditional medicine were an unreliable predictor of whether those extractions would be suitable for further experimental work. From our initial set of 111 tissue samples, 81 sequencing reactions were successful and 55 of those sequences had species-level matches to COI reference sequences on the NCBI GenBank and/or BOLD databases. Molecular identification revealed that traditional health practitioners correctly labelled 77% of the samples that we successfully identified with DNA barcoding in this study. Our mixed methodology approach is useful for conservation planning as it updates knowledge of animal use in Indigenous remedies and can accurately identify species of high conservation priority. Furthermore, this study highlights the possibility of collaborative conservation planning with traditional health practitioners.

The Isolation and Characterization of Bacteriophages Infecting Avian Pathogenic Escherichia coli O1, O2 and O78 Strains.

Avian pathogenic Escherichia coli (APEC), such as O1, O2 and O78, are important serogroups relating to chicken health, being responsible for colibacillosis. In this study, we isolated and characterized bacteriophages (phages) from hen feces and human sewage in Alberta with the potential for controlling colibacillosis in laying hens. The lytic profile, host range, pH tolerance and morphology of seven APEC-infecting phages (ASO1A, ASO1B, ASO2A, ASO78A, ASO2B, AVIO78A and ASO78B) were assessed using a microplate phage virulence assay and transmission electron microscopy (TEM). The potential safety of phages at the genome level was predicted using AMRFinderPlus and the Virulence Factor Database. Finally, phage genera and genetic relatedness with other known phages from the NCBI GenBank database were inferred using the virus intergenomic distance calculator and single gene-based phylogenetic trees. The seven APEC-infecting phages preferentially lysed APEC strains in this study, with ECL21443 (O2) being the most susceptible to phages (n = 5). ASO78A had the broadest host range, lysing all tested strains (n = 5) except ECL20885 (O1). Phages were viable at a pH of 2.5 or 3.5-9.0 after 4 h of incubation. Based on TEM, phages were classed as myovirus, siphovirus and podovirus. No genes associated with virulence, antimicrobial resistance or lysogeny were detected in phage genomes. Comparative genomic analysis placed six of the seven phages in five genera: Felixounavirus (ASO1A and ASO1B), Phapecoctavirus (ASO2A), Tequatrovirus (ASO78A), Kayfunavirus (ASO2B) and Sashavirus (AVIO78A). Based on the nucleotide intergenomic similarity (<70%), phage ASO78B was not assigned a genus in the siphovirus and could represent a new genus in class Caudoviricetes. The tail fiber protein phylogeny revealed variations within APEC-infecting phages and closely related phages. Diverse APEC-infecting phages harbored in the environment demonstrate the potential to control colibacillosis in poultry.

Identification of four autochthonous yeasts from the intestines of goldfish, Carassius auratus with potential probiotic properties and their effects on the most common fish bacterial pathogens

In aquaculture, probiotic yeasts have gained particular interest because of their numerous health benefits for farmed fish. Many autochthonous yeasts have been isolated and identified from fish species with potential probiotic characteristics. In the present study, four autochthonous yeast strains were identified and characterized from the intestinal tracts of 16 healthy goldfish, Carassius auratus. Their in vitro probiotic properties were examined in terms of cell surface hydrophobicity, co-aggregation, and tolerability to different pH values and bile salt concentrations. These strains were identified by culture characters and sequence analysis of ITS (Internal Transcribed Spacer) gene regions. Four strains, namely Cutaneotrichosporon jirovecii isolate jpn01, Debaryomyces nepalensis isolate jpn02, Blastobotrys proliferans isolate jpn05, and Diutina catenulata isolate jpn06, were identified and added to the NCBI GenBank with accession numbers defined as MT584874.1, MT584873.1, MT649918.1, and MT501155.1, respectively. Results demonstrated the capability of these strains to co-aggregate with several fish-associated bacterial pathogens such as Lactococcus garvieae, Vagococcus salmoninarum, Vibrio anguillarum, Yersinia ruckeri, and Aeromonas hydrophila. Only the jpn05 strain did not co-aggregate with A. hydrophila. All identified yeast isolates could grow and tolerate low pH conditions (pH 2.0) and bile salt concentrations (up to 1.5%). Of interest, the hydrophobicity (%) of the yeast isolates was 80%, 94.0%, 80.6%, and 66.4% for jpn01, jpn02, jpn05, and jpn06 isolates, respectively. In this context, our data provide important in vitro evidence for the potential probiotic features of the yeast isolates. These strains could be considered candidate probiotic yeasts; however, their application in aquaculture nutrition necessitates further in vivo assays.

Diversity, Antimicrobial, Antioxidant, and Anticancer Activity of Culturable Fungal Endophyte Communities in Cordia dichotoma.

Endophytic fungi are a significant source of secondary metabolites, which are chemical compounds with biological activities. The present study emphasizes the first-time isolation and identification of such fungi and their pharmacological activities from the medicinal plant Cordia dichotoma, which is native to Jammu, India. The Shannon Wiener diversity index revealed a wide range of fungal endophytes in root (1.992), stem (1.645), and leaf (1.46) tissues. A total of 19 endophytic fungi belonging to nine different genera were isolated from this plant and the majority belonged to the Ascomycota phylum. ITS rRNA gene sequencing was used to identify the fungal strains and they were submitted in NCBI GenBank. The most potent fungal isolate Cladosporium cladosporioides OP870014 had strong antimicrobial, antioxidant, and anticancer activity against MCF-7, HCT-116, and PC-3 cancer cell lines. The LC-MS and GC-MS analyses of the ethyl acetate extract of C. cladosporioides were examined to identify the bioactive metabolites. The major compounds of the crude extract derived from C. cladosporioides OP870014, according to GC-MS, are spiculisporic acid; dibutyl phthalate; phenylethyl alcohol; cyclohexanone, 2,3,3-trimethyl-2-3-methylbutyl; pyrrolo[1,2-a]pyrazine-1,4-dione,hexahydro-3-(phenylmethyl);2,5-piperazinedione,3,6-bis(2-methylpropyl); and heneicosane which possessed antimicrobial, anticancerous, and antioxidant activities. The findings revealed that C. dichotoma has the capacity to host a wide variety of fungal endophytes and that secondary metabolites from the endophytic fungus may be a source of alternative naturally occurring antimicrobial, antioxidant, and cytotoxic compounds.

First report of Ceratocystis ficicola causing wilt disease on common fig (Ficus carica) in Italy.

Common fig (Ficus carica L.) in is one of the most important crops in the Mediterranean area. In Italy, it is grown on a total area of 2118 ha. In Apulia (South-eastern Italy), the annual production of fig exceeds 3200 tons annually and together with olive and grapevine, they characterize the Apulian agricultural panorama. In September 2021, symptoms of a vascular wilt disease and, in severe cases, decline tree mortality were observed in Salento area (Apulia). Symptomatic Affected plants showed symptoms of leaf wilt and different stages of disease expression, which begins with leaf chlorosis on shoots, followed by wilting, extensive defoliation and twig dieback. On the main branches andlower part of the trunk and in some cases on lateral branches, bark cracks and cankers were observed and extended wood discoloration was detected in cross sections. In two orchards located in Salice Salentino (Site 1) and Squinzano (Site 2), where disease incidence exceeded 80%, 3-5 wood discs per tree were gathered from affected tissues from two (Site 1) and four (Site 2) trees. Isolations were performed on malt extract agar 2% amended with 0.5 g L-1 streptomycin sulfate. A Ceratocystis species was recovered from all samples trees with high frequencies (83.3%). Two-week-old colonies on potato dextrose agar showed black ascomata with 300-600 µm wide bases and 1100-2250 µm long necks. On the tips of the necks, ascospores (5-6x4-5 µm) exuded in creamy white sticky masses. Endoconidia (5-9x4.5-7 µm) were abundant, cylindrical, aseptate, and produced in chains. Two monoconidial representative strains CRSFA.Cer.033 (Site 1) and CRSFA.Cer.035 (Site 2) were deposited in the DISSPA Di.S.S.P.A. collection of the University of Bari. Species identification was done through sequence analyses of rDNA internal transcribed spacer region (ITS) using ITS5/ITS4 primers (White et al. 1990), elongation factor 1 alpha gene (TEF) using EF1/EF2 (O'Donnell et al. 1998) and RNA polymerase II gene (RPB2) gene using RPB2-5F/FRPB2fRPB2-7cR (Liu et al. 1999). Sequences were deposited in NCBI GenBank (accession numbers: OQ329983-OQ335969 (ITS), OQ352265-OQ352266 (TEF), OQ352268-OQ352267 (RPB2)). The sequences of both Apulian isolates were identical. BLAST searches revealed high similarity to the sequences of two isolates of Ceratocystis ficicola Kajitani and Masuya from Japan: ex-type CMW38543 and CMW38544, specifically 98.41% identity matching with KY685076 (ITS), 100% with KY685079 (TEF), and 99.87% with KY685083 and KY685082 (RPB2). Pathogenicity tests were conducted, on six common fig 'Dottato' seedlings by inoculating one year-old twigs with mycelium plugs (Bolboli et al. 2022). Control plants were inoculated with PDA plugs without mycelium. After one month, all inoculated twigs showed symptoms of wilt. Forty days post-inoculation, the bark of inoculated twigs was removed, and longitudinal and transverse sections revealed wood discolorations extending above and below the inoculation point. Ceratocystis ficicola was consistently reisolated from symptomatic tissues and identified as described above, thus fulfilling Koch's postulates. Neither symptoms nor positive isolations were observed in control seedlings. The pathogen was first described in 2011 in Japan (Kajitani and Masuya, 2011) where it currently affects all fig-producing areas. In 2018, it was reported for the first time in the EPPO region in Greece (Tsopelas et al., 2021), and to our knowledge, this is the first report on its detection in Italy. Since February 2022, C. ficicola has been included in the EPPO alert list because of its potential to cause tree mortality and the difficulty of its eradication. Regional national surveys are therefore urgently needed to determine its distribution in the fig growing areas of Italy and limit its spread. References Bolboli, Z., et al. 2022. Mycol. Prog. 21:89. doi: 10.1007/s11557-022-01834-9 Kajitani, Y., and Masuya, H., 2011. Mycoscience 52:349. doi: 10.1007/s10267-011-0116-5 Liu, Y. J., et al. 1999. Mol. Biol. and Evol. 16:1799. doi: 10.1093/oxfordjournals.molbev.a026092 O'Donnell, K., et al. 1998. Proc Natl Acad Sci USA 95:2044. doi: 10.1073/pnas.95.5.2044 Tsopelas, P., et al. 2021. Phytopathol. Mediterr. 60:337. doi: 10.36253/phyto-12794 White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego. doi: 10.1016/0307-4412(91)90165-5.

First report of Alternaria burnsii causing leaf spot on Bletilla striata in China.

Bletilla striata (named "Bai Ji" in Chinese) is a plant from the Orchidaceae family that has been employed in traditional Chinese medicine for thousands of years in China. Polysaccharides extracted from B. striata have been shown to have an effect on Alzheimer's disease (Lin et al. 2021). Since 2021, leaf spots have been observed in the B. striata plantation in Chongqing, China. Out of 200 plants, the disease incidence was estimated at 56%, and the disease index was estimated at 32%. The symptoms were necrotic lesions with brown edges and yellow halos; severe infection caused the infected leaves to become blighted, dry and fall off. To identify the causal agent, eighteen leaves with typical symptoms were collected from the B. striata plantation (30.60°N, 108.64°E). The margins of infected tissue areas were cut into small pieces (5×5 mm), surface sterilized with 70% ethanol for 1 min, and rinsed twice with sterile distilled water. The tissue was then surface sterilized in 3% sodium hypochlorite for 2 min, followed by three rinses with sterile water. The tissue was then placed onto potato dextrose agar (PDA) plates and incubated at 25°C for 3 days, pure cultures of fungal isolates were obtained by single-spore isolation, stored on PDA slants and maintained at 4°C. Colonies of the fungal isolates showed three color types, ranging from grayish white to green above with olive green on the reverse, but conidial characteristics were more similar and indicated this was a single fungus. Conidiophores were single, lateral from hyphae or terminal; straight or curved; smooth-walled with 1 to 8 septa; pale brown; usually with only one pigmented terminal conidiogenous site, sometimes with one additional lateral conidiogenous locus; sometimes slightly swollen at the apex; and 15 to 170 μm long, 2.5 to 4.5 μm wide. Conidia were in short or moderately long chains of 2-8 conidia normally, sometimes with more; rarely branched; normally 14.07 to 50 × 5.24 to 10 μm in size; ellipsoid, fusiform, long ellipsoid, obclavate or ovoid with 1 to 11 transverse septa and 2 to 4 longitudinal septa; beakless or with subcylindric or cylindric secondary conidiophores, analogous to the beak 4.25 to 58.6 μm long, 3.2 to 4.8 μm wide. The fungal isolates were tentatively identified as Alternaria sp. The representative isolate BJ8 was selected for the pathogenicity test. The leaves of six healthy plants of B. striata (two years old) grown in pots were washed with sterile water. Ten mL of conidial suspension (1×106 conidia mL-1) contained in 0.05% Tween 80 buffer was brushed onto upper and lower surfaces of all the leaves on three plants, while other plants were brushed with 10 mL 0.05% Tween 80 buffer to serve as controls. Plants were placed in a greenhouse at 25°C and 95±1% relative humidity after inoculation and observed for symptoms. The symptoms initially developed as irregular brown necrotic lesions on the inoculated leaves after 7 days, with a yellow halo around the lesions, consistent with the symptoms in the field. Leaves on the control plants did not produce any symptoms. For molecular identification, the genomic DNAs of representative isolates BJ5, BJ6, and BJ8 were extracted. The internal transcribed spacer (ITS) region and RNA polymerase II second largest subunit (RPB2), translation elongation factor 1-alpha (TEF1), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes were used for polymerase chain reaction (PCR), using primers ITS5/ITS4, GPD1/GPD2, EF-1F/EF-1B and RPB27cR/RPB25F2, respectively (White et al. 1990; Berbee and Pirseyedi et al. 1999; Carbone and Kohn 1999; Liu et al. 1999). The neighbor-joining tree revealed that these isolates are clustered together with the reference strain of A. burnsii. The sequences were deposited in NCBI GenBank BJ5 [ITS: OP897263; GAPDH: OQ544937; TEF1: OQ544941; RPB2: OQ544939], BJ6 [ITS: OP897262; GAPDH: OQ544938; TEF1: OQ544942; RPB2: OQ544940], and BJ8 [ITS: OK285209; GAPDH: OK340046; TEF1: OK340047; RPB2: OQ544936]. All three isolates showed 100% similarity with A. burnsii CBS 107.38 [ITS: KP124420; GAPDH: JQ646305; TEF1: KP125198; RPB2: JQ646457] ex-type sequence, thus the pathogen causing the leaf spot on B. striata was identified as A. burnsii. A. burnsii is an important pathogenic fungus causing blight of cumin (Shekhawat et al. 2013). Furthermore, Al-Nadabi et al. (2018) found that A. burnsii can cause leaf spots on wheat and date palms, and Sunapao et al. (2022) reported that A. burnsii can infect coconuts (Cocos nucifera), causing dirty panicle disease. This is the first report of A. burnsii causing leaf spot on B. striata in China. The new discovery shows that since A. burnsii can readily adapt to a variety of climatic conditions, controlling the fungus is crucial for the healthy growth of B. striata in the future. This study will provide a basis for further elucidating the pathogenic mechanism and development of effective control measures for this disease.

First report of areolate mildew of cotton, caused by Ramulariopsis pseudoglycines in Mississippi.

In August of 2022, cotton (Gossypium hirsutum L.) growing in several north central Mississippi counties was observed to exhibit yellowish lesions on the adaxial leaf surface with white powdery fungal growth on the corresponding abaxial surface. By the end of the 2022 growing season, 19 Mississippi counties were observed to have infected cotton. Symptomatic leaves were collected from affected plants, sealed in plastic freezer bags, stored on ice in a cooler, and transported to the laboratory. Prior to isolation, the pathogen was microscopically examined and determied to be morphologically similar to the description of Ramulariopsis spp. (Ehrlich and Wolf 1932). Using a sterile needle, conidia were transferred to V8 medium amended with chloramphenicol (75 mg/liter) and streptomycin sulfate (125 mg/liter) and incubated in the dark at 25°C. After 14 days, the colony diameter was measured, and morphological characteristics were consistent with previous descriptions (Videira et al. 2016; Volponi et al. 2014). On V8 medium, the 7 mm diameter colonies grew raised, lumpy, and lobed, with iron-grey coloration. The mycelia were hyaline, septate, branched, and 1 to 3 μm in diameter. Conidia ranged from 2.8 to 25.6 μm in length and 1.0 to 4.9 μm in width (x = 12.8 × 3.1 μm; n = 20). Pure cultures were obtained on V8 medium, and DNA was extracted from a 14-day-old-culture. TW098-22, a representative isolate, was amplified, and sequenced targeting the internal transcribed spacer (ITS), translation elongation factor 1-α (TEF 1-α), and actin (ACT) genes as described by Videira et al. (2016). The consensus sequences were deposited in GenBank (accession no. OQ653427, OR157986, OR157987). BLASTn query of the NCBI GenBank showed 100% identity of the 483-bp (ITS) and 706-bp TEF 1-α sequences from TW098-22 with Ramulariopsis pseudoglycines CPC 18242 (type culture; Videira et al. 2016). Koch's postulates were performed after multiplying individual colonies by streaking on V8 medium as above. Culture plates were subsequently incubated at 25°C for 14 days in the dark. Colonies were aseptically transferred to 50 ml centrifuge tubes containing 50 ml of autoclaved reverse osmosis (RO) water amended with Tween 20 (0.01%). The resulting inoculum suspension was adjusted to 13.5 × 105 conidia/ml using a hemocytometer. The foliage of five, 25-day-old cotton plants were sprayed with 10 ml of the suspension and a plastic bag was placed over each plant to maintain humidity for 30 days. Five plants were sprayed with sterilized RO water to serve as controls. Plants were incubated in a growth chamber at 25°C and ~70% relative humidity with 16:8 h of light:dark. Thirty days post-inoculation, foliar symptoms and signs were observed on all inoculated plants including small necrotic lesions and white powdery growth. Control plants remained asymptomatic. The trial was repeated. When reisolated, the colony and conidia morphology and DNA sequence (ITS) were consistent with the description of the original field isolate. Areolate mildew of cotton can be caused by two species of Ramulariopsis: R. gossypii and R. pseudoglycines (Videira et al. 2016). The two species have been reported in Brazil (Mathioni et al. 2021); however, this is the first report of R. pseudoglycines in the United States. In addition, even though areolate mildew has previously been reported from much of the southeastern U.S. (Anonymous 1960), the report herein serves as the first description of R. pseudoglycines in Mississippi and U.S. cotton.

Genetic variation of sequencing 18srDNA gene of Trichophyton mentagrophytes isolates

Background. Trichophyton species are considered the most frequent causative and considerable agents in infection concerns. Objective. The existing training designed to conduct the sequencing analysis of nucleotides of ITS1-5.8S-ITS2 for Trichophyton mentagrophytes. Methods. The isolation and identification of pathogenic fungi, Trichophyton mentagrophytes from clinical specimens was done based on the standard morphological and molecular methods. The genomic DNA of fungal isolates were extracted and purified to amplify with primers of 18S rRNA gene for detection and sequencing the nitrogenous bases to define the genetic variation among clinical isolates of Trichophyton mentagrophytes in compared with strains recorded in NCBI GenBank. Results. Eight isolates of Trichophyton mentagrophytes were isolated and identified from clinical specimen of dermatophytosis. The DNA sequencing analysis showed the presence of some genetic variation in nitrogenous bases between the local isolates and that recorded in locus of world NCBI GenBank. Multiple Alignment sequence using NCBI BLAST revealed the recoding a new mutant isolate among the local isolates based on DNA homology percent. Conclusion. The present results proved the successful the use of molecular methods in diagnosis the fungal isolates of Trichophyton mentagrophytes especially the sequencing analysis to find the genetically bases of these isolates.

Phylogenetic analysis among some species of aphids (Homoptera: Aphididae) using DNA sequencing moleculartechnique

The phylogeny of aphids (Hemiptera: Aphididae) has been studied by molecular technique for the first time in Kurdistan, this study comprises relationship between six species of Aphids collected from the leaves of different plants (Chrysanthemum, Oak, Almond, Pine, Asteraceae and Herbaceous) in many localities of Erbil governorate Kurdistan region-Iraq, started in May to July 2022. For understanding about aphid evolution, phylogenetic of aphid is crucial. However, neither the phylogenetic alterations of the Aphid taxa nor their comprehensive definition have been achieved. Therefore, a unique method has been developed in this study to examine COI gene sequencing and infer the relationships between the major aphid taxa. DNA was isolated, and a band of 550 bp of mt COI gene was amplified. Then the amplicons were sequenced. The part of the COI gene of the insect samples are alignment inside of NCBI GenBank by BLAST program, were used to compare our nucleotide have sequenced with other stored species of insect sequences. This research presented that studying phylogeny of aphid species through a sequencing technique can create a phylogenetic tree for the used species with reliable results. So, our species in Kurdistan region clustered in a monophyletic clade with published from most countries with high identic value (100%). The COI sequence of aphid species were submitted to GenBank with six accessions of OP355287 - OP355292. The composition of nucleotides of the sequence of COI gene was low of G-C base pairing. We were successful in showing that the mt-COI gene can be used as a molecular marker for the identification of related species, as shown by the similarities between the phylogenetic association created by COI

MOLECULAR IDENTIFICATION OF THRIPS SPECIES, WHICH INFESTS THE GREENHOUSE VEGETABLES INCLUDING EGGPLANT IN THE CENTRAL AGRARIAN REGION OF MONGOLIA

In Mongolia, the first record of onion thrips was informed in vegetable fields by D. Tsedev (Tsendsuren et al., 1979), since that has no detailed research materials relating to the identification of thrips and the Thysanoptera group observed in different crop fields. In 2017–2019, we have taken the thrips samples from the following areas, which spread on eggplant, cucumber, tomato, paprika, and beans grown in the greenhouses of the Agropark research and training center, the greenhouses of the Bornuur soum in the Tuv province and the Mandal soum of Selenge province and onion field accordingly. The mitochondrial COI gene of selected insect samples has been used for species identification. For the nucleotide sequence of the mitochondrial COI area of the insects, we amplified with universal LCO1490 and HCO2198 primers. We have illustrated the COI gene fragments of thrips samples. For building a phylogenetic tree was constructed using the Neighbor-Joining method. A bootstrap test with 1000 replications was carried out. The evolutionary distances were calculated using Tamura’s three-parameter method. A phylogenetic tree was built for 14 sequences with a total length of 681bp nucleotides. When conducting phylogenetic analysis using the MEGA X program, it was displayed the phylogenetic origin of our samples in all inferred trees is the same as the Chinese species; Thrips tabaci (China – Zhejiang), which registered with MN036455 accession number in the gene bank of NCBI. According to these results, the sampled thrips were collected from various vegetables including eggplants in Mongolia identified as Thrips tabaci and we have registered it in the GenBank of NCBI under OP288232 accession number. Keywords. Eggplant damage, thrips species identification, COI gene, phylogenetic origin, PCR.

Morphological and Molecular Identification of Adoretus hirsutus (Ohaus, 1914) (Coleoptera:Scarabaeidae:Rutelinae) from Erbil Governorate Kurdistan Region- Iraq

This study provides a detailed description of Adoretus hirsutus (Ohaus, 1914) (Coleoptera:Scarabaeidae: Rutelinae), as a first record in Iraq. Between March and July 2022, we collected specimens from various weed flowers in different locations within the Erbil Governorate, Kurdistan Region, Iraq. According to molecular analysis, Adoretus hirsutus was used as a source of samples for PCR amplification of the fragments (710 bp) of the mtCOI gene for phylogenetic analysis. To compare the nucleotide sequence with those of other insect species, a section of the mtCOI gene from the collected insect was aligned with the NCBI GenBank database using the BLAST tool. The BLAST results showed that the second record in the NCBI GenBank identity of insects. The COI sequence of Adoretus hirsutus was submitted to GenBank with accession numbers OQ4288117, OQ428818, and OQ428819. The morphological diagnostic characteristics of the species are; Labrum nearly cup shaped, lateral margins moderately concave with a row of small spines, median apical projection overhanging the mentum. Mandibles irregular shaped, apically with single oval shaped tooth. Terminal maxillary palpomere 1.5 times as long as the 2nd. Antenna brown, consisting of 10 antennomeres ending in a unilateral three lamellated club, equal in length. Outer margin of fore tibia with three acute teeth. Aedagaeus moderately curved, parameres elongated oval, apical part is very acute. Some important parts such as labrum, mandible, antenna, fore legs, elytra, pygidium and male genitalia have been photographed.

Research on Passiflora foetida L. as a Pharmaceutical Treatment for Neurasthenia in Humans.

&lt;b&gt;Background and Objective:&lt;/b&gt; This plant is known in many parts of the world and is used as medicine in some countries. In Vietnam, people know how to use &lt;i&gt;Passiflora foetida &lt;/i&gt;L.,&lt;i&gt; &lt;/i&gt;as an herb. There are many research works in the world, most of them focus on medicinal properties. The objective of this study was to determine the genetic diversity of samples of &lt;i&gt;Passiflora foetida &lt;/i&gt;L., yellow fruit based on agronomic traits and the gene region of "&lt;i&gt;rbcL&lt;/i&gt;". &lt;b&gt;Materials and Methods:&lt;/b&gt; Seed samples were arranged in a completely randomized design with three replications. The trial was a sample of &lt;i&gt;Passiflora foetida &lt;/i&gt;L., species. The distance between sample plant is 3×2 m, so the total number of trees is 1,330 trees ha&lt;sup&gt;1&lt;/sup&gt;. The genetic relationship between them was determined through the construction of a phylogenetic tree in the "&lt;i&gt;rbcL&lt;/i&gt;" gene region sequence. Data analysis and processing methods done by using X software. &lt;b&gt;Results:&lt;/b&gt; The PCR results that amplify the "&lt;i&gt;rbcL&lt;/i&gt;" gene region around 670 bp, the PCR products were then sequenced. The sequence results were compared with the sequences on the NCBI gene bank, showing that the sequences of the nine varieties/species all coincided with the &lt;i&gt;Passiflora foetida &lt;/i&gt;Sims species sequences with a high similarity coefficient from 98.77 to 99.9%. Genetically shows that all nine species samples belong to &lt;i&gt;Passiflora foetida&lt;/i&gt; which can be classified into three genetic samples of An Giang (LA1), Ca Mau (LA2) and Can Tho (LA3) which are genetically close to each other, have the same index. &lt;b&gt;Conclusion:&lt;/b&gt; The heritability in the broad sense is high in the two traits of stem height and leaf length, so it can be considered that these two traits are controlled by genes. The cultivation of algae seeds to improve the productivity of these medicinal plant varieties is important in providing raw materials for the oriental medicine industry.

First Report of Peanut Black Pod Rot Caused by Berkeleyomyces rouxiae in China.

Peanut (Arachis hypogaea L.) is an important oilseed and cash crop cultivated in over 100 countries worldwide. The major producers are China, India and USA (Ding et al. 2022). In September 2022, peanut pods exhibiting black necrotic symptoms on the shell surface were observed in Puyang, Henan Province, China. These black spots often merged to form larger necrotic spots on the shell. Disease incidence was 100% in susceptible varieties. Symptomatic shell pieces were surface sterilized with 75% ethanol for 3 min, rinsed three times with sterile water, and then transferred onto PDA medium supplemented with 25 µg/ml chloramphenicol (Long et al. 2022). Isolation frequency of a fungus with similar-appearing colonies from symptomatic pods was 81.7%. A pure culture of a representative isolate, PYHB, was obtained through single-sporing and maintained on PDA plates at 25℃ in darkness. The colony initially appeared white but turned black within 2 days. The isolate produced dark brown, unicellular chlamydospores, which were arranged in club-shaped chains consisting of two to seven cells. The size of the unicellular chlamydospores varied from 3.34 to 15.27 µm (average:6.81, n = 100) in length and 8.30 to 15.51 µm (average:11.29, n = 100) in width. The endoconidia were hyaline and cylindrical, measuring 7.91-22.94 × 1.69-4.81 µm (average: 12.16 × 3.13, n = 100). Based on morphological characteristics, the isolate was tentatively identified as a Berkeleyomyces sp. (Nel et al. 2018; Long et al. 2022). The ITS region of r-DNA, the ribosomal large subunit (LSU), the minichromosome maintenance complex component 7 (MCM7), and the 60S ribosomal protein RPL10 (60S) genes were amplified using ITS1/ITS4, LR0R/LR5, rouxMCM7-F/rouxMCM7-R and roux60s-F/roux60s-R primers, respectively (White et al. 1990; Vilgalys and Hester 1990; Nakane and Usami 2020). The sequences were deposited in GenBank (ITS: OR053803; LSU: OR053818; MCM7: OR058549; 60S: OR060656). Through BLASTn analysis of the NCBI GenBank database, the generated ITS and LSU sequences showed 100% identity to Berkeleyomyces rouxiae (GenBank MF952418.1 and MF948662.1, respectively) and B. basicola (GenBank MT221585.1 and MH868639.1, respectively). Importantly, the MCM7 and 60S sequences were 100% identical to B. rouxiae (GenBank MF967114.1 and MF967077.1, respectively). Phylogenetic analysis combining ITS, LSU, MCM7, and 60S sequences showed that the isolate PYHB clustered with B. rouxiae. To evaluate pathogenicity, surface-sterilized healthy peanut pods (n = 90) were immersed in a 1×106 spore/ml conidial suspension obtained from isolate PYHB for 5 min and placed in Petri dishes containing moistened cotton at 25°C for 10 days. Pods (n = 90) inoculated with sterile water served as controls. Inoculated pods displayed black necrosis 10 days after inoculation (dai), whereas no symptoms were observed on the control pods at 21 dai. The reisolated pathogen was shown to be identical to the original inoculum through morphological and phylogenetic analysis. Black root rot is a fungal disease caused by Berkeleyomyces spp. (syn. Thielaviopsis spp.) and affects various crops and ornamentals, such as cotton, tobacco, carrot, holly, and pansy (Rahnama et al. 2022). The causal agents B. rouxiae and B. basicola have similar morphological characteristics but can be differentiated through molecular characterization (Nel et al. 2018). To our knowledge, this is the first report of black pod rot in peanut caused by B. rouxiae in China. The finding from this study will contribute to the development of monitoring and management strategies to combat this destructive disease in peanut cultivation.

Studies on Symptomatology, Morphological and Molecular Characterisiation of Erysiphe cichoracearum Causing Powdery Mildew of Okra

Okra (Abelmoschus esculentus (L.) Moench) is a globally important annual vegetable belongs to family malvaceae, it is most broadly distributed vegetable all over the world. Among the fungal diseases affecting okra crop, powdery mildew caused by Erysiphe cichoracearum DC. is the most important disease causing considerable yield losses. The disease was characterized by the appearance of small white powdery specks on upper surface of the lower leaves which enlarged and coalesced forming bigger patches. Later on the disease spread to the upper leaves, coalescing of the white powdery specks and enlargement in their size ultimately resulted in complete coating of white fungal mass on the leaves. The morphological studies of the pathogen in the laboratory revealed, that the mycelium is septate, ectophytic, hyaline and adjacent to the mycelium, basal septum of the conidiophores was seen. The conidiophores were erect, on which conidia were produced either singly or in short chains. The conidia were found cylindrical or barrel in shape, hyaline, non-septate and measured 75.23 µm x 40.65 µm. Molecular characterisation of the native isolate resulted in the DNA amplicon at the region 531 bp. Further, DNA sequence was obtained for ITS Rdna and was deposited in NCBI gene bank. Accession number ‘MW774352’ was obtained and it was confirmed that the causal pathogen of okra powdery mildew of Raichur region is Erysiphe cichoracearum.

A duplex nested RT-PCR method for monitoring porcine epidemic diarrhea virus and porcine delta-coronavirus

BackgroundPorcine epidemic diarrhea virus (PEDV) and porcine delta-coronavirus (PDCoV) are economically important pathogens that cause diarrhea in sows and acute death of newborn piglets. Moreover, the emerging PDCoV was reported to infect children. The current situation is that vaccine prevention has not met expectations, and emergency containment strategies following outbreaks cannot prevent the damages and losses already incurred. Therefore, a more sensitive detection method, that is both convenient and enables accurate and effective sequencing, that will provide early warning of PEDV and PDCoV is necessary. This will enable active, effective, and comprehensive prevention and control, which will possibly reduce disease occurrences.ResultsDuplex nested RT-PCR (dnRT-PCR) is an ideal method to achieve early warning and monitoring of PEDV and PDCoV diseases, and to additionally investigate any molecular epidemiological characteristics. In this study, two pairs of primers were designed for each virus based upon the highly conserved N protein sequences of both PEDV and PDCoV strains retrieved from the NCBI Genbank. After optimization of the reaction conditions, the dnRT-PCR assay amplified a 749-bp fragment specific to PEDV and a 344-bp fragment specific to PDCoV. Meanwhile, the specificity and sensitivity of the primers and clinical samples were tested to verify and establish this dnRT-PCR method. The limit of detection (LoD)for both PEDV and PDCoV was 10 copies/µL. The results showed that among 251 samples, 1 sample contained PEDV infection, 19 samples contained a PDCoV infection, and 8 samples were infected with both viruses, following the use of dnRT-PCR. Subsequently, the positive samples were sent for sequencing, and the sequencing results confirmed that they were all positive for the viruses detected using dnRT-PCR, and conventional RT-PCR detection was conducted again after the onset of disease. As these results were consistent with previous results, a detection method for PEDV and PDCoV using dnRT-PCR was successfully established. In conclusion, the dnRT-PCR method established in this study was able to detect both PEDV and PDCoV, concomitantly.ConclusionsThe duplex nested RT-PCR method represents a convenient, reliable, specific, sensitive and anti-interference technique for detecting PEDV and PDCoV, and can additionally be used to simultaneously determine the molecular epidemiological background.

Identification of Lasiodiplodia species inciting stem rot of dragon fruit in India through polyphasic approach.

Lasiodiplodia species commonly thrive as endophytes, saprobes, and plant pathogens in tropical and subtropical regions. Association of Lasiodiplodia species causing stem rot in dragon fruit in the coastal belt of Odisha, eastern India, has been illustrated here. The stem rot disease was characterized by yellowing of the stem, followed by softening of the stem tissues with fungal fructifications of the pathogen in the affected tissues. On the basis of macro- and micromorphological characteristics, the four fungal isolates recovered from diseased stems were identified initially as Lasiodiplodia species. By comparing DNA sequences within the NCBI GenBank database as well as performing a multigene phylogenetic analysis involving the internal transcribed spacer region (ITS-rDNA), β-tubulin (β-tub), and elongation factor-alpha (EF1-α) genes, the identity of Lasiodiplodia isolates was determined. The isolate CHES-21-DFCA was identified as Lasiodiplodia iraniensis (syn: L. iranensis) and the remaining three isolates, namely CHES-22-DFCA-1, CHES-22-DFCA-2, and CHES-22-DFCA-3, as L. theobromae. Although pathogenicity studies confirmed both L. iraniensisand L. theobromae were responsible for stem rot in dragon fruit, L. iraniensis was more virulent than L. theobromae. This study established the association of Lasiodiplodia species with stem rot in dragon fruit using a polyphasic approach. Further investigations are required, particularly related to on host-pathogen-weather interaction and spatiotemporal distribution across the major dragon fruit-growing areas of the country to formulate prospective disease management strategies. This is the first report on these two species of Lasiodiplodia inflicting stem rot in Hylocereus species in India.