Sequences Of Internal Transcribed Spacer Region Research Articles

Morphological and Molecular Characterization of the Pathogen Associated with Infected Leaf and Fruits of Tomato

This investigation describes the morpho-molecular characterization of the pathogen associated with infected leaf and fruits of tomato (Solanum lycopersicum L.). The fungal pathogen was identified based on their cultural morphology, microscopic features and analysis of Internal Transcribed Spacer (ITS) region sequences of nuclear ribosomal DNA (nrDNA). Cultural morphology including colour of the young and mature colony, growth pattern, concentric rings etc. and microscopic features including shape and size of microconidia, macroconidia, phialide, shape of apical and basal cells of macroconidia, septation in conidia, inter-septal distance and formation of chlamydospores corroborated the identity with the pathogenic fungi Fusarium oxysporum. The phylogenetic analysis based ITS regions sequences of nrDNA of the fungal isolate showed 100% identity with Fusarium oxysporum. Thus the ITS of nrDNA sequences validated the morphological data. Pathogenicity test also reconfirmed the identity of the test isolate of Fusarium oxysporum. The Chittagong Univ. J. B. Sci.,Vol. 10(1 &2):31-40, 2020.

Morphological and Molecular Characterization of the Pathogen Associated with Infected Leaf and Fruits of Tomato

This investigation describes the morpho-molecular characterization of the pathogen associated with infected leaf and fruits of tomato (Solanum lycopersicum L.). The fungal pathogen was identified based on their cultural morphology, microscopic features and analysis of Internal Transcribed Spacer (ITS) region sequences of nuclear ribosomal DNA (nrDNA). Cultural morphology including colour of the young and mature colony, growth pattern, concentric rings etc. and microscopic features including shape and size of microconidia, macroconidia, phialide, shape of apical and basal cells of macroconidia, septation in conidia, inter-septal distance and formation of chlamydospores corroborated the identity with the pathogenic fungi Fusarium oxysporum. The phylogenetic analysis based ITS regions sequences of nrDNA of the fungal isolate showed 100% identity with Fusarium oxysporum. Thus the ITS of nrDNA sequences validated the morphological data. Pathogenicity test also reconfirmed the identity of the test isolate of Fusarium oxysporum. The Chittagong Univ. J. B. Sci.,Vol. 10(1 &2):31-40, 2020.

Comparative expression profile of selected genes in Venturia inaequalis Cooke (Wint.) infecting apple fruits and leaves

Scab is a noxious fungal disease of apples (Malus domestica Borkh) in all apple producing regions caused by a host-specific phytopathogen Venturia inaequalis Cooke (Wint.). Its symptoms include black or brown lesions on leaves as well as on fruits, and causes fruit deformation. In this study, V. inaequalis was isolated from infected fruit samples and expression level of selected pathogenesis related genes in scab infected fruits and leaves was studied. The isolated fungus formed a brown coloured mat-like colony having septate mycelium and produced acute ovoid shaped conidia. Molecular characterization of the fungus was done by amplification and sequencing of internal transcribed spacer (ITS) and Cytochrome (CYP51A1) regions of the isolate. The Sanger sequencing of amplicons and sequence analysis using BLAST tool of the NCBI against GenBank database confirmed that the obtained sequence of ITS and CYP51A1 regions had 99.6 % and 98 % sequence identity with the reference V. inaequalis, respectively. The isolated strain of V. inaequalis was submitted in the fungal repository of Microbial Type Culture Collection (MTCC), India. The phylogenetic analysis of ITS region of the isolate revealed that the isolated strain of V. inaequalis was more closely related to Fusicladium eriobotryae compared to other Venturia species. The expression levels of pathogenesis related genes viz. CIN1, CE5 and VICE16 were higher in infected leaves as compared to infected fruits. Whereas expression of VICE12 and GH28 were higher in infected fruits compared to infected leaves. VICE4 gene showed equal level of expression during infection in both fruits and leaves, which was also maximum as compared to the control treatment. The transcript analysis of aforementioned genes of V. inaequalis gives the insights of the pathogen's expression profile during pathogenesis in fruits and leaves. This expression analysis can form a basis selecting pathogenesis related genes as targets for developing dsRNA expressing constructs with an aim to reduce RNAi mediated silencing of specific genes, in a futuristic biotechnological based solution to deal with apple scab disease.

Phenotypic Characteristics, Pathogenicity, and Molecular Identification of Hypomyces perniciosus Causing Wet Bubble Disease of Edible Mushrooms

Abstract The research aimed to determine the phenotypic characteristic, pathogenicity and molecular characterization of Hypomyces perniciosus isolates responsible for wet bubble disease of the white button mushroom Agaricus bisporus. Phenotypic characteristics such as colony appearance, mycelium texture, and pigmentation were studied on four different agar media, i.e., potato dextrose agar (PDA), malt extract agar (MEA), Czapek-Dox yeast agar (CYA), and Sabouraud dextrose agar (SDA), after eight days of incubation. Additionally, the growth rate of the tested isolates was studied depending on the pH of the medium. Fungal isolates showed the highest mycelial growth on MEA and SDA at pH 6.0. However, on CYA at pH 7.0, the mycelium exhibited the worst growth. Isolate identification and genetic relationship analysis were carried out using internal transcribed spacer region sequencing and the random amplified polymorphic DNA method. The research confirmed that all Polish isolates belong to the species H. perniciosus, and the genetic diversity is relatively low. Phylogenetic analyses revealed three subgroups of H. perniciosus isolates. The first group included three genetically distinct isolates with a similarity coefficient in the range of 0.76–0.85 to isolates CBS 815.73 and CBS 322.52. The second group was divided into two subgroups and included 16 isolates with a genetic similarity range of 0.91 to 1.0 to CBS 815.73 and CBS 322.52 isolates. Furthermore, the eight genetically similar isolates exhibited the greatest pathogenicity towards A. bisporus.

First Report of Agroathelia rolfsii Causing Southern Blight on Cowpea in China

Cowpea (Vigna unguiculata L.) is a legume consumed as a high-quality plant protein source in many parts of the world. In August 2023, it was observed that a plant disease affected cowpea growth in Yiyang (28.34°N, 112.55°E), China. The average disease incidence was 10%, resulting in 8.5% economic losses in approximately 3,000 m2. The symptoms initially appeared as brown lesions near the stem-soil interface and the lesions were colonized by white mycelia. As the disease progressed, the disease symptoms included constriction and brown staining at the base of the stem, covered with a small amount of white mycelia. Eventually, the entire plants withered and collapsed and many sclerotia were scattered on the ground around the diseased stem. Twenty samples (10 sclerotia and 10 diseased tissue fragments) were collected from symptomatic plants for causal agent isolation. Samples were disinfected with 70% ethanol for 30 s, 5% NaClO for 1 min, rinsed three times with sterile water, dried and placed on potato dextrose agar (PDA) plates at 28℃ in the dark. In total, 20 isolates were obtained by the hyphal tip method (Terrones et al. 2022) and showed a consistent phenotype of white cottony mycelia on PDA with an growth rate of 12.9 to 21.3 mm/day (n = 20). Sclerotia formed at five to eight days post inoculation, were initially whitish, turning beige and eventually dark brown. The diameter of mature sclerotia ranged from 0.89 to 2.13 mm (mean = 1.64±0.29 mm; n =50). For pathogen identification, ITS1/ITS4 (White et al. 1990) and EF1-983F/EF1-2218R (Rehner and Buckley 2005) primers were used to amplify the internal transcribed spacer regions (ITS) and translation elongation factor-1 alpha gene (TEF-1α), respectively. The sequences of all 20 isolates showed 99% to 100% similarity with Agroathelia rolfsii sequences from GenBank by BLAST analysis. The sequences of two representative strains, ID1 and ID4, were deposited in GenBank. The ITS sequences of ID1 (OR689482) and ID4 (OR689481) were ＞99% similar to A. rolfsii strain QJ7 (593/596 bp; MZ750983) and A. rolfsii strain Kale078 (565/568 bp; MN872304), respectively. Also, TEF-1α sequences of ID1 (OR713735) and ID4 (OR713736) were ＞99% similar to the sequences of A. rolfsii strain HS-Sr (1073/1073 bp; OL416131) and A. rolfsii strain MSB1-2 (1070/1075 bp; MN702790), respectively. Phylogenetic analysis based on ITS and TEF1-α sequences indicated that ID1 and ID4 clustered into the A. rolfsii clade. Based on morphology and sequence analyses, the isolates ID1 and ID4 were identified as A. rolfsii (anamorph Sclerotium rolfsii). Pathogenicity tests were conducted three times on healthy 30-day-old cowpea seedlings. Five plants were inoculated with 6-day-old mycelial discs (6 mm) of ID1 or ID4 at the base of the seedlings (n = 30) while four plants were inoculated with a sterile PDA disc as a control (n = 12). All seedlings were cultivated in a greenhouse with a temperature of 26°C to 28°C and relative humidity 60% to 80% with a 14/10 h light/dark photoperiod. Eight days later, all the fungal inoculated seedlings showed symptoms including brown necrosis and collapse of the stems, and eventual withering of the seedlings. Control plants remained asymptomatic. The causal pathogens were reisolated in PDA plates and identified by ITS sequence analysis, completing Koch's postulates. To our knowledge, this is the first report of A. rolfsii causing southern blight on cowpea in China. Early accurate diagnosis will help farmers to adopt suitable practices to control disease outbreaks and reduce losses.

First report of Powdery Mildew Caused by Podosphaera xanthii on Siraitia grosvenorii in Guizhou, China.

Swingle (Siraitia grosvenorii), a member of the Cucurbitaceae family, stands out as a distinctive plant with both economic and medicinal significance. In October 2023, severe powdery mildew were observed on S. grosvenorii in Guiyang City (26.50°N; 106.66°E), Guizhou Province, China. About 80 % of the plants in the greenhouse showed powdery mildew symptoms. Three infected plant samples were selected for morphological and molecular analysis (GZAAS 23-0801, GZAAS 23-0802 and GZAAS 23-0803). The voucher specimens are deposited in the Key Laboratory of Agricultural Biotechnology of Guizhou Province. The symptoms initially manifested as irregular to nearly circular, small yellow spots, with distinct depressions as well as surfaces covered in white mycelium. Over time, these spots gradually expanded and merged patches. In the final stages, the entire leaves turned into yellow and withered. Microscopic observations showed that fungal hyphae were septate, branched, and flexuous to straight and 5 to 9 µm wide, and appressoria were indistinct to slightly nipple-shaped. Conidia were hyaline and ellipsoid to oval with fibrosin bodies and measured 31 to 43 × 18 to 24 μm (n = 50) with a length/width ratio of 1.3 to 2.3. Conidiophores were unbranched, straight, 120 to 268 × 14 to 22 µm (n = 30), producing two to five immature conidia in chains. Foot cells of conidiophores were cylindrical, 39 to 84 × 8 to 14 μm (n = 30), followed by one to three short cells. Short cells were cylindrical, 12 to 32 × 8 to 15 μm (n = 50). The morphological characteristics were identical with the previous description of Podosphaera xanthii (Braun and Cook, 2012). Total DNA was extracted from conidia and mycelia by the Chelex method (Walsh et al., 1991). The ribosomal DNA internal transcribed spacer (ITS) and nuclear ribosomal large subunit (LSU) were amplified by using the primers ITS1/ITS4 (White et al., 1990) and LSU1/LSU2 (Scholin et al., 1994), respectively. The ITS (OR825802, OR825803 and OR825804, respectively) and LSU (OR825805, OR825806 and OR825807, respectively) sequences of three isolates, were deposited in GenBank. The BLAST results revealed that both the ITS and LSU region sequence were 100% identical to those of P. xanthii (ITS: MF043939, MG754404 and KJ698669; LSU: OQ061319, AB936277and OP218411). Phylogenetic analyses of ITS and LSU sequences showed that our three isolates were clustered with P. xanthii (KX842351, LC270782 and LC270779) with high statistical support (ML/MP/BI: 100%/97%/1.00). Combined with their morphological characteristics, these three isolates were identified as P. xanthii. Pathogenicity tests were performed by gently brushing conidia onto the leaves of five healthy S. grosvenorii plants. Five non-inoculated plants were used as the control. All plants were maintained in a greenhouse at 25 ± 2°C. One week after inoculation, similar symptoms were observed in the inoculated plants, whereas no symptoms occurred on the control plants. By microscopic observation, the fungus on the inoculated plants was morphologically identical to those on originally diseased plants. Powdery mildew caused by P. xanthii has been reported on Vernonia cinerea (Wu et al., 2023), Vigna unguiculata (Zhang et al., 2023), Cucumis melo (Meesam et al., 2023). To our knowledge, this is the first report of powdery mildew caused by P. xanthii on S. grosvenorii in Guizhou, China. The occurrence of powdery mildew on S. grosvenorii may pose a potential threat to its large-scale cultivation. The pathogen could become a threat to other Cucurbitaceae members in the future.

First report of Truncatella angustata causing leaf blight on Thuja plicata Donn ex D. Don in Canada.

Western redcedar (Thuja plicata Donn ex D. Don) is one of the most important commercial tree species in British Columbia, generates more than $1 billion in economic activity annually and about 8-10 million trees are planted in reforestation efforts (Gregory et al. 2018). It has been selected as the provincial tree of British Columbia (BC) because of its tremendous economic, ecoogical and cultural value. However, foliar diseases such as leaf blights have serious impact on redcedar growth and may cause significant loss of tree volume (Russell, 2007). Our 2014 - 2015 surveys of western redcedar forests in coastal areas of BC indicated high incidence of a distinctive type of blight. We observed the incidence of this disease on more than 80% of western redcedar (approximately 493) trees from late May to early December. Early symptoms appeared as circular to oval, brownish to black spots (2-3 mm), 1-5 spots per branch tip, scattered at the tip margins. Sequentially, the spots enlarged and developed into necrotic lesions on both young and old leaves. More than 50 symptomatic leaves from 10 different trees were collected and rinsed in distilled water then surface-sterilized with three times washing in Tween 20 (%5 solution) for 2 minutes (each time) and %70 ethanol for 30 second (3 times repeat). Tissues from under lesions were placed on MEA (Malt Extract Agar; Phyto Tech® labs-Product ID: M498) and PDA (Potato Dextrose Agar; Phyto Tech® Labs-Product ID: P772). The plates were incubated at 21°C in the dark. They developed distinct dull white to brown, cottony colonies with each black acervuli approximately 450-500µm. The isolates produced fusiform conidia with four cells. They didn't have any distinct color. The conidiophore size was approximately 23-24 x 2-3 µm with mostly hyaline to light brown color, branched and conidiogenous was hyaline and not branched and simple. The spore size was approximately 15-20μm by 7-10μm with three transverse septa and endogenous papillae with hyaline apical appendages. Next, we collected spores and replated them on fresh MEA media culture and placed back in the incubator to produce pure cultures. We studied conidia from leaves of trees mentioned above using light and electron microscopy using Hitachi S-3500N Scanning Electron Microscope (Noshad et al. 2023). After morphological study, further identification to the species level conducted using Zambounis and Wenneker's approach (Zambounis 2019; Wenneker,2017). Genomic DNA from two single-spore isolates were isolated and sequenced. Sequences of ITS (Internal Transcribed Spacer) region amplified using primers ITS1/ITS4 and sequenced. Final sequences were deposited in Genbank and published (accession numbers OP086244 and OP086251). Blast analysis of these sequences showed 99% and 99% resemblances with T. angustata sequence (Sutton 1980). To verify its pathogenicity, we performed a comprehensive pathogenicity test to fulfill Koch's postulates. We collected their distinctive spores in an aseptic environment and standardized them (5000/ml) using a haemocytometer. Then we inoculated 100 western redcedar seedlings (three years old) by injecting standardized spore suspension solution (inoculum) using ultra-fine 0.3ml, 31G, 8mm syringes (approximately 0.1ml per inoculation site). Ten positive control seedlings were inoculated with distilled water and ten negative control seedlings were not inoculated at all. All inoculated (experimental) seedlings demonstrated same symptoms (black spots and characteristic spores) after eight weeks. None of the control seedlings showed any similar symptoms. In the next stage, we isolated and cultured spores from inoculated seedlings and studied them. The identity of reisolates confirmed using DNA sequencing. We used these spores for our next set of disease screening which was successful again. We identified Truncatella angustata (Pers.) Hughes as the causal agent for shoot-tip blight (STB) on western redcedar by examining morphological and molecular characteristics of the pathogen. This is the first report of T. angustata as a primary pathogen on western redcedar in British Columbia, Canada.

First Report of Charcoal Rot Caused by Macrophomina phaseolina on Dry Bean (Phaseolus vulgaris L.) in Western Canada.

In 2021, several dry bean (Phaseolus vulgaris L.) plants at the mid-seed-fill growth stage displaying wilting, chlorosis of the leaves and reduced vigor were collected near the Pembina - Emerson Border of Manitoba, Canada and North Dakota, USA. When symptomatic plants were examined, gray to dark brown discoloration was observed on the lower stem and the roots. Afterwards, brown to black discoloration was noticed on stem and root sections. Root and lower stem pieces (1 to 2 cm) from affected plants were surface sterilized with 70 % ethanol, followed by 1% NaOCl, rinsed twice in sterilized water, air dried on sterilized filter papers, and placed on potato dextrose agar (PDA) amended with 1 mg/mL of streptomycin sulfate. The PDA plates were incubated at 28°C with 12 h light/12 h dark for 10 days. The growing hyphae were transferred using the hyphal tip method to new PDA plates. Growing cultures were initially hyaline and turned from light gray to dark brown or black with age. Abundant dark and spherical to oblong shaped sclerotia with an average diameter of 97.9 µm (range: 66.8 to 143.5 µm, n =30) formed on the pure cultures 7 days after incubation. Additional pure culture was obtained through an isolation of a single microsclerotium followed by a single hyphal tip transfer. One isolate was identified as Macrophomina phaseolina based on morphological characteristics (Smith and Wyllie 1999). The morphological identity was confirmed by sequencing the rDNA internal transcribed spacer (ITS) region with universal primers ITS1/ITS4 (White et al. 1990) and calmodulin (CAL) and translation elongation factor-1 alpha (TEF-1α) genes with MpTefF/MpTefR, and MpCalF/MpCalR primer sets (Santos et al. 2020), respectively. The online resource Basic Local Alignment Search Tool (BLAST; https://www.ncbi.nlm.nih.gov/BLAST) confirmed the fungus identity as 100% M. phaseolina. The sequences of the original isolate BF21-25 were deposited in GenBank with accession numbers OQ615297 (ITS), OR357630 (CAL), and OR363106 (TEF-1α). To confirm pathogenicity, bioassays were conducted under controlled conditions. Four seeds of cultivar 'Etna' were sown per pot, and five pots were used for inoculated (approx. 4 × 105 microsclerotia/pot) and control (mock-inoculated with sterile PDA medium) treatments. For the inoculum, 20 g of macerated 10 to 14-day old M. phaseolina culture grown on PDA medium was applied to each pot using an inoculum layering technique. Pots were kept in the greenhouse with 28/17°C day/night, 13 h light/11 h dark cycle, and 70% relative humidity and watered weekly. Disease symptoms similar to those observed in the field were visible on all inoculated plants at the mid-seed-fill growth stage. Mock-inoculated control plants didn't show any symptoms. The experiment was repeated twice with similar results. The pathogen was re-isolated from infected plants to confirm Koch's postulates and identified as M. phaseolina based on the morphology and sequences of ITS, CAL and TEF-1α regions. To our knowledge, this is the first report of charcoal rot caused by M. phaseolina on dry bean in Western Canada.

Leaf Spot of Hedychium coronarium Caused by Colletotrichum gloeosporioides in China

Hedychium coronarium (white ginger) is widely cultivated for garden decoration and folk medicine. Since 2020, symptomatic leaves showed brown necrosis and yellow borders on H. coronarium in the field (approximately 200 m2) at Southwest University, Rongchang District, Chongqing City. Small brown-yellow spots gradually enlarged and caused withering in severe cases with a mortality rate of around 10%. Disease incidence and severity varied from 55 to 65% and from 30 to 40%, respectively. Infected tissues (5 mm in diameter) were cut from lesion margins, surface sterilized in 70% ethanol for 10 s and 0.1% acidic mercuric chloride for 3 min, followed by rinsing in sterile water three times, and then were cultured onto potato dextrose agar (PDA) at 25 °C. Five isolates were transferred onto fresh PDA and purified by single-spore culturing. The colonies were initially white and turned hoary, and the diameter reached 32.95 to 38.37 mm × 32.42 to 38.61 mm after 3 days of incubation. Pale gray abundant fluffy aerial mycelia were arranged irregularly and densely. Hyphae were septate and branched, 2 to 5 µm in width. Conidiophores were pale brown, septate, branched, cylindrical to ampulliform. Conidia were hyaline, smooth-walled, cylindrical with obtuse ends, and 8.1 to 13.3 μm × 2.4 to 5.8 μm (n = 50) in size. Appressoria were medium brown to dark brown, aseptate, in irregular shape, solitary or in groups, and measured 1.5 to 12.5 μm × 2.1 to 13.3 μm. Morphological characteristics of isolates agreed with the description of Colletotrichum (Liu et al. 2015). Genomic DNA was extracted from fungal colonies incubated on PDA for 7 days following the instructions from the PlantGen DNA Kit (CWBIO, China). The internal transcribed spacer (ITS) region, and fragments of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), beta-tubulin (TUB2) and large subunit ribosomal DNA (LSU rDNA) genes were amplified by primer pairs ITS1/ ITS4, GDF1/GDR1, ACT512F/ACT783R (Naz et al. 2017), T1/Bt2b (Glass et al. 1995) and LROR/LR7 (Castlebury et al. 2002), respectively. The sequence of representative isolate CG-H (GenBank accession nos. OM010355, OM238213, OM238214, OM045778 and OM010358 for ITS, GAPDH, ACT, TUB2 and LSU rDNA, respectively) exhibited 99 to 100% identity to Colletotrichum gloeosporioides. A multi-locus phylogenetic tree with concatenated sequences of ITS, GAPDH, ACT and TUB regions was constructed using the maximum likelihood method by MEGA7, which revealed that strain CG-H was grouped with C. gloeosporioides. To confirm the pathogenicity, six healthy H. coronarium plants were surface sterilized, and conidial suspension (1 × 106 conidia/mL) was sprayed onto the leaves. Six plants were inoculated with sterile distilled water as controls. All the plants grew in a greenhouse at 25 °C under 12 h/12 h photoperiod. The experiment was repeated four times. Yellow lesions appeared after 7 days of inoculation, irregular-shaped brown spots were formed and slightly sunken within 14 days, and the whole leaf gradually became withered in 50 days. All inoculated plants exhibited leaf spot symptoms while the control plants remained asymptomatic. C. gloeosporioides was re-isolated from lesions of leaves and identified by morphology and sequence analysis, fully confirming Koch’s postulates. This is the first report of C. gloeosporioides associated with H. coronarium leaf spot in China and worldwide. Further studies will be conducted on the sensitivity of C. gloeosporioides to various fungicides.

Use of the its Region in the Identification of Endophytic Mycota in Fruits of Syagrus Coronata (MART.) BECC., Caatinga Bioma

Objective: The study aimed to identify the endophytic fungi present in fruits of S. coronata (licuri) through sequencing of the ITS (Internal transcribed spacer) region. Theoretical framework: The Syagrus coronata palm tree, known as licuri, plays a significant role in the Caatinga, both in socioeconomic and cultural terms. The fruits of this plant host several types of fungi, including saprophytes, phytopathogens, and endophytes. The complexity of fungi taxonomic identification, due to the diversity and morphological similarity between distinct taxa, often requires the use of molecular biology as an essential tool for accurate characterization. Method: The study used 14 isolates of endophytic fungi from fruits of S. coronota (licuri) preserved in the Mycoteca of the Mycology Laboratory of the Universidade do Estado da Bahia/DEDC - Campus VIII, Paulo Afonso. The DNA of these isolates was extracted to perform PCR (Polymerase Chain Reaction) using the primers ITS1F and ITS4. The PCR products were sequenced and analyzed with the Blastn tool, revealing 98 to 100% similarity in the accessions. Results and conclusion: From the 14 isolates, four presented themselves as Chlamydospores and one as Mycelia sterilia, making morphological identification unfeasible, and four were from taxa without taxonomic identification. The taxa identified using ITS region sequencing belong to the genera Curvularia, Diplodia, Fusarium, Lasiodiplodia, Neodeightonia, and Penicillium. Research implications: This study highlights the importance of using molecular techniques to complement the taxonomy based on morphological markers. Originality/value: The primary purpose of this study was to use the ITS region as a tool for identifying endophytic fungi in licuri fruits, since in the literature the mycota of this botanical substrate, which is a biocultural heritage of Bahia, is practically unknown.

First report of powdery mildew on Vigna unguiculata caused by Podosphaera xanthii in China.

Vigna unguiculata belongs to the Legume family, and is an annual twining, herbaceous vine plant, which is native to Africa. V. unguiculata is the most economically beneficial type of off-season vegetables in Hainan, China because of its rich in nutrients such as protein, minerals, dietary fiber, and vitamins (Jayathilake et al. 2018). In April 2022, typical powdery mildew infection was observed on V. unguiculata leaves in Haikou, Hainan Province, China (20°3'40.428"N, 110°19'45.217"E). More than 70% leaves of 13 V. unguiculata plants displayed severe powdery mildew disease. The diseased leaves at first exhibited white rounded irregular patches, which gradually enlarged, fused and covered all the leaf as well as stems. Edges of the infected leaves crinkled upwards, and the leaves often fell off the plants at the late infection stage. On the infected leaves, many conidiophores and dense mycelium were observed by microscopic analysis. Hyphae were septate, branched, epigenous, and flexuous to straight. Hyphal appressoria were indistinct or slightly nipple-shaped, and the haustoria developed were in the shape of oval-sphere and 9 to 11μm long. Foot cells of conidiophores were straight, cylindrical, and measured 43 to 70 × 10 to 12 μm. The conidiophores arising straightly from a hyphal cell, were measured 168 to 252 (mean = 204) μm in length and produced 6 to 9 immature conidia in each chain. Conidia were ovate, pyriform or barrel-shaped, with fibrosin bodies, and measured 26 to 32 (mean = 29.4) × 16 to 20 (mean = 18.6) μm. The chasmothecia was not found in all samples. These morphological characteristics were typical of the conidial stage of the powdery mildew Podosphaera xanthii of genus Podosphaera (Braun and Cook 2012). To further confirm the identity of this causal fungus, the internal transcribed spacer (ITS) region, and the partial sequence of large subunit ribosomal RNA gene (28S rRNA), were amplified with primer pairs ITS1/ ITS4 (White et al. 1990) and NL1/NLP2 (Mori et al. 2000) from extracted genomic DNA. The obtained 563-bp ITS region and 715-bp 28S rRNA gene sequences were deposited in GenBank (ITS, OQ415534; 28S rRNA, OQ415545.1), and were compared with BLAST analysis in the GenBank nr database. The results revealed that the ITS region sequence was 99.82% identity with P. xanthii isolate HUVU-08 (MH143485.1), and the 28S rRNA gene partial sequence was 100% identity with P. xanthii isolate XHL1 (MK357442.1). On the basis of the morphological characteristics and sequence analysis, this fungus was identified as P. xanthii. Pathogenicity tests were performed by gently brushing conidia onto the leaves of six healthy potted V. unguiculata plants. Six non-inoculated plants were used as control. All plants were maintained in a greenhouse at 26 ± 2°C. After 2 weeks inoculation, similar symptoms were observed in the inoculated plants, whereas no symptoms occurred on the control plants. By microscopic observation, the fungus present on the inoculated plants was morphologically identical to those on originally diseased plants. Furthermore, ITS and 28S rRNA sequences of the re-isolated fungus individually displayed 100% identity with OQ415534 and OQ415545.1. So far, although powdery mildew disease caused by P. xanthii on different plants including Sigesbeckia orientalis (Mukhtar et al. 2022), Vigna radiata (Sheu et al. 2021), Cosmos bipinnatus (Kong et al. 2023), Verbena brasiliensis (Luecke et al. 2020), Cucurbita ficifolia (Choi et al. 2022), Glandularia tenera (Pei et al. 2023) and Verbena bonariensis (Choi et al. 2023) have been reported, to our knowledge, this is the first report of powdery mildew caused by P. xanthii on V. unguiculata in Hainan, China, which seriously threatens the utilization of V. unguiculata on off-season vegetables industry.

Yueomyces silvicola sp. nov., a novel ascomycetous yeast species unable to utilize ammonium, glutamate, and glutamine as sole nitrogen sources.

Five yeast strains isolated from tree bark and rotten wood collected in central and southwestern China, together with four Brazilian strains (three from soil and rotting wood collected in an Amazonian rainforest biome and one from Bromeliad collected in Alagoas state) and one Costa Rican strain isolated from a flower beetle, represent a new species closely related with Yueomyces sinensis in Saccharomycetaceae, as revealed by the 26S ribosomal RNA gene D1/D2 domain and the internal transcribed spacer region sequence analysis. The name Yueomyces silvicola sp. nov. is proposed for this new species with the holotype China General Microbiological Culture Collection Center 2.6469 (= Japan Collection of Microorganisms 34885). The new species exhibits a whole-genome average nucleotide identity value of 77.8% with Y. sinensis. The two Yueomyces species shared unique physiological characteristics of being unable to utilize ammonium and the majority of the amino acids, including glutamate and glutamine, as sole nitrogen sources. Among the 20 amino acids tested, only leucine and tyrosine can be utilized by the Yueomyces species. Genome sequence comparison showed that GAT1, which encodes a GATA family protein participating in transcriptional activation of nitrogen-catabolic genes in Saccharomyces cerevisiae, is absent in the Yueomyces species. However, the failure of the Yueomyces species to utilize ammonium, glutamate, and glutamine, which are generally preferred nitrogen sources for microorganisms, implies that more complicated alterations in the central nitrogen metabolism pathway might occur in the genus Yueomyces.

Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing

Among molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), is commonly used in clinical routine laboratories due to its simplicity, universality, efficacy, and affordability for fungal species identification. However, Sanger sequencing fails to identify mixed ITS sequences in the case of mixed infections. To overcome this limitation, different high-throughput sequencing technologies have been explored. The nanopore-based technology is now one of the most promising long-read sequencing technologies on the market as it has the potential to sequence the full-length ITS region in a single read. In this study, we established a workflow for species identification using the sequences of the entire ITS region generated by nanopore sequencing of both pure yeast isolates and mocked mixed species reads generated with different scenarios. The species used in this study included Candida albicans (n = 2), Candida tropicalis (n = 1), Nakaseomyces glabratus (formerly Candida glabrata) (n = 1), Trichosporon asahii (n = 2), Pichia kudriavzevii (formerly Candida krusei) (n = 1), and Cryptococcus neoformans (n = 1). Comparing various methods to generate the consensus sequence for fungal species identification, the results from this study indicate that read clustering using a modified version of the NanoCLUST pipeline is more sensitive than Canu or VSEARCH, as it classified species accurately with a lower abundance cluster of reads (3% abundance compared to 10% with VSEARCH). The modified NanoCLUST also reduced the number of classified clusters compared to VSEARCH, making the subsequent BLAST+ analysis faster. Subsampling of the datasets, which reduces the size of the datasets by approximately tenfold, did not significantly affect the identification results in terms of the identified species name, percent identity, query coverage, percentage of reads in the classified cluster, and the number of clusters. The ability of the method to distinguish mixed species within sub-populations of large datasets has the potential to aid computer analysis by reducing the required processing power. The herein presented new sequence analysis pipeline will facilitate better interpretation of fungal sequence data for species identification.

First Report of Alternaria alternata Causing Leaf Spot on Broccoli in Ecuador.

In Ecuador, broccoli (Brassica oleracea var. italica) production is located in the Andean region, specifically Cotopaxi-Ecuador (INEC, 2019). A leaf pathogen has been constantly observed in this area, showing brown circular necrosis surrounded by yellowish halo-like spots causing leaf death (Fig. 1a). This pathogen was believed to be Alternaria sp.; however, the species was not determined either using classical or molecular tools. In 2021, ten leaves showing similar symptoms were collected in Cotopaxi and sent for pathogen identification. Here, leaf explants (0.25 cm2) showing disease symptoms were surface sterilized with 2% sodium hypochlorite (NaClO) and 70% ethanol (C2H6O), rinsed with sterile water, and transferred to Potato Dextrose Agar (PDA) media. Petri dishes were incubated in darkness at 25°C for five days. The single hyphal tip method was used to purify the cultures on PDA. Fifteen pure isolates were obtained after incubating for 14 days. Isolates were incubated under blacklight for two days to induce fungal sporulation. All isolates presented early white cotton-like mycelium that later became dark green (Fig 1b). Under the microscope, we observed straight primary conidia in simple or branched chains. Also, the conidia were obclavate, long ellipsoids, moderate in size (19.5-43.9 μm in length, 7.1-17.2 μm in width), and septate with few longitudinal septa. Lastly, the conidium body can narrow itself into a secondary conidia (Fig 1c) (Woudenberg et al., 2013). According to colony and conidia morphology, isolates were identified as Alternaria sp. (Woudenberg et al., 2013). Five isolates were randomly selected for DNA extraction and sequencing of ITS (internal transcribed spacer; Chou, H.H. and Wu, W.S. 2002), TEF (translation elongation factor; O'Donnell et al., 1998), and RPB2 (RNA polymerase II second largest subunit; Liu et al., 1999) gene regions. DNA sequences obtained from each marker were identical for all isolates. Consensus sequences and alignment were built using ClustalX in MEGA X (Kumar et al., 2018). Consensus sequences were deposited in GenBank with the following accession numbers: ITS, ON982232; TEF, ON983964; RPB2, ON983963. A multilocus Bayesian inference phylogenetic tree was constructed in Beast software (version 1.8.4) using the concatenated sequences (Drummond et al., 2012; Maharachchikumbura et al., 2014). The isolates in our study clustered with isolates of Alternaria alternata, confirming their identity (Figure 2). For Koch's postulates, healthy broccoli plants were grown in sterile soil for six weeks. The fungal conidia were suspended in sterile distilled water (1×106 conidia/ml), and the leaves were inoculated by spraying the spore solution. The control treatment was sprayed with sterile distilled water alone. Plants were maintained at 28°C and had more than 85% relative humidity (Sigillo et al., 2020). Seven days after inoculation, plants showed chlorosis and necrosis. Ten days later, 100% of the treated leaves presented brown circular necrosis (Fig. 1d). Control plants showed no disease symptoms. Re-isolation of the pathogen from the diseased leaf tissue was performed as previously described. The isolates presented the exact morphology of pure cultures obtained from field-diseased leaves. The pathogenicity test was performed twice. To our knowledge, this is the first report on A. alternata being the causal agent of leaf spot on broccoli in Ecuador. Disease diagnosis contributes to providing strategies against this pathogen. Further investigations are needed to find biological/chemical techniques or cultivar resistance to control this pathogen in broccoli.

Morphological characteristics and nucleotide sequence of ITS region and rbcL gene of Cu cang native taro

Cu cang taro cultivar in Thuan Chau district, Son La province is a precious indigenous genetic resource with high quality and well adapted to the characteristic natural conditions of Thuan Chau district, Son La province of Vietnam. However, Cu cang taro has been mixed with different cultivars in the locality. In this article, the authors presented morphological characteristics and nucleotide sequence of ITS(Internal Transcribed Spacer) region and rbcL gene of Cu cang taro in Thuan Chau district, Son La province. The ITS region and rbcL sequences isolated from Cu cang taro had sizes 506 and 630 bp. The results of similarity comparison on NCBI identified the DNA isolated from the ITS region, the rbcL gene of Cu cang taro is Colocasia esculenta species. The rbcL gene of Cu cang taro has 99.27% similarity with Colocasia esculenta var. antiquorum.

First Report of Charcoal Rot Caused by Macrophomina phaseolina on Stevia rebaudiana in Arizona, USA.

Stevia (Stevia rebaudiana Bertoni) is an important medicinal crop grown worldwide. Leaves of stevia contain a non-caloric sweetener, stevioside, which is used as a substitute to artificial sweeteners. In August 2022, symptoms of chlorosis, wilting, and root rot were observed in about 30 % of stevia plants growing at the Agricultural Station at Yuma Agricultural Center, Yuma, AZ, USA (32.7125° N, 114.7067° W). Infected plants initially showed chlorosis and wilting, and the plants eventually died with foliage remaining intact to the plant. Cross sections of the crown tissue of affected stevia plants showed necrotic tissue and a dark brown discoloration in areas of the vascular and cortical tissues. Dark brown microsclerotia were observed on stem bases and necrotic roots of the infected plants. Five symptomatic plants were sampled to isolate the pathogen. Root and crown tissues (0.5 to 1 cm) were surface disinfested with 1% sodium hypochlorite for 2 min, rinsed three times with sterile water, and plated onto potato dextrose agar (PDA). All the five isolates displayed rapid mycelial growth on PDA at 28°C with a 12-h photoperiod. The mycelia were initially hyaline and turned from gray to black after 7 days. Masses of dark spherical to oblong microsclerotia were observed after 3 days on PDA, measuring an average of 75 µm width × 114 µm length (n=30). For molecular identification, genomic DNA was extracted from mycelia and microsclerotia of a representative isolate (Yuma) using the DNeasy Plant Pro kit (Qiagen, Hilden, Germany). The internal transcribed spacer (ITS), translation elongation factor-1α (TEF-1α), calmodulin (CAL), and β-tubulin (β-TUB) regions were amplified using the primer sets, ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone and Kohn 1999), MpCalF/MpCalR (Santos et al. 2020), and T1/T22 (O'Donnell and Cigelink 1997), respectively. A BLAST search of sequences revealed 98.7 to 100% identity to Macrophomina phaseolina sequences (MK757624, KT261797, MK447823, MK447918). Both morphological and molecular characteristics confirmed the fungus as M. phaseolina (Holliday and Punithaligam 1970). Sequences were submitted in the GenBank under accession numbers OP599770 (ITS), OP690156 (TEF-1α), OP612814 (CAL), and OP690157 (β-TUB). Pathogenicity assay was performed on 9-week-old stevia plants (var. SW2267), grown in 4-inch planters in the greenhouse. The inoculum was made from a 14-day-old culture of M. phaseolina grown in conical flasks (250 ml) in potato dextrose broth at 28°C. Mycelial mats of the fungus were blended in 250 ml of sterile distilled water, filtered through four layers of cheesecloth, and then calibrated to 105 microsclerotia/ml using a hemocytometer. Twenty healthy plants were inoculated by soil drenching 50 ml of the inoculum per pot. Soil drenching using sterile distilled water was done on 5 non-inoculated control plants. Plants were maintained in the greenhouse at 28 ± 3°C with 12 h photoperiod. After 6 weeks, necrosis at the base of petioles and chlorosis of the leaves, followed by wilting were noticed on all 20 inoculated plants, whereas all the 5 control plants remained healthy. The fungus was reisolated and identified as M. phaseolina based on the morphology and sequences of ITS, TEF-1α, CAL and β-TUB regions. Although M. phaseolina has been reported earlier on stevia in NC, USA (Koehler and Shew 2018), this is a first report from AZ, USA. M. phaseolina is known to be favored by high soil temperatures (Zveibil et al. 2011), thus represents a potential threat to stevia production in AZ, USA in coming years.

Wide variation of heterozygotic genotypes of recent fasciolid hybrids from livestock in Bangladesh assessed by rDNA internal transcribed spacer region sequencing and cloning

Fascioliasis causes high economic losses in livestock and underlies public health problems in rural areas, mainly of low-income countries. The increasing animal infection rates in Bangladesh were assessed, by focusing on host species, different parts of the country, and rDNA sequences. Fasciolid flukes were collected from buffaloes, cattle, goats and sheep from many localities to assess prevalences and intensities of infection. The nuclear rDNA internal transcribed spacer (ITS) region including ITS-1 and ITS-2 spacers was analyzed by direct sequencing and cloning, given the detection of intermediate phenotypic forms in Bangladesh. The 35.4% prevalence in goats and 55.5% in buffaloes are the highest recorded in these animals in Bangladesh. In cattle (29.3%) and sheep (26.8%) prevalences are also high for these species. These prevalences are very high when compared to lowlands at similar latitudes in neighboring India. The high prevalences and intensities appear in western Bangladesh where cross-border importation of animals from India occur. The combined haplotype CH3A of Fasciola gigantica widely found in all livestock species throughout Bangladesh fits its historical connections with the western Grand Trunk Road and the eastern Tea-Horse Road. The “pure” F. hepatica sequences only in clones from specimens showing heterozygotic positions indicate recent hybridization events with local “pure” F. gigantica, since concerted evolution did not yet have sufficient time to homogenize the rDNA operon. The detection of up to six different sequences coexisting in the cloned specimens evidences crossbreeding between hybrid parents, indicating repeated, superimposed and rapidly evolving hybridization events. The high proportion of hybrids highlights an increasing animal infection trend and human infection risk, and the need for control measures, mainly concerning goats in household farming management. ITS-1 and ITS-2 markers prove to be useful for detecting recent hybrid fasciolids. The introduction of a Fasciola species with imported livestock into a highly prevalent area of the other Fasciola species may lead to a high nucleotide variation in the species-differing positions in the extremely conserved fasciolid spacers. Results suggest that, in ancient times, frequent crossbreeding inside the same Fasciola species gave rise to the very peculiar characteristics of the present-day nuclear genome of both fasciolids.

Description of lipase producing novel yeast species Debaryomyces apis f.a., sp. nov. and a modified pH indicator dye-based method for the screening of lipase producing microorganisms

Four yeast strains were isolated from the gut of stingless bee, collected in Churdhar, Himachal Pradesh, India. Physiological characterization, morphological examination, and sequence analysis of small subunit ribosomal RNA (18S rRNA) genes, internal transcribed spacer (ITS) region, and D1/D2 domain of the large subunit rRNA gene revealed that the four strains isolated from the gut of stingless bee belonged to the Debaryomyces clade. Strain CIG-23HT showed sequence divergence of 7.5% from Debaryomyces nepalensis JCM 2095T, 7.8% from Debaryomyces udenii JCM 7855T, and Debaryomyces coudertii JCM 2387T in the D1/D2 domain. In the ITS region sequences, strain CIG-23HT showed a 15% sequence divergence from Debaryomyces nepalensis JCM 2095T and Debaryomyces coudertii JCM 2387T. In 18S rRNA gene sequence, the strain CIG-23HT showed 1.14% sequence divergence from Debaryomyces nepalensis JCM 2095 and and Debaryomyces coudertii JCM 2387, and 0.83% sequence divergence from Debaryomyces hansenii NRRL Y-7426. Strain CIG-23HT can utilize more carbon sources than closely related species. The findings suggest that strain CIG-23HT is a novel species of the genus Debaryomyces, and we propose to name it as Debaryomyces apis f.a., sp. nov. The holotype is CBS 16297T, and the isotypes are MTCC 12914T and KCTC 37024T. The MycoBank number of Debaryomyces apis f.a., sp. nov. is MB836065. Additionally, a method using cresol red and Bromothymol blue pH indicator dyes was developed to screen for lipase producers, which is more sensitive and efficient than the currently used phenol red and rhodamine B dye-based screening methods, and avoids the problem of less differentiable zone of hydrolysis.

First report of Fusarium fujikuroi causes leaf spot in Polygonatum odoratum (Mill.) Druce in China.

Polygonatum odoratum (Mill.) Druce, a member of Liliaceae, is one of the traditional Chinese herbal plants mainly used in Jilin, Hubei, Guangxi, Zhejiang, Liaoning, Hunan and Guangdong provinces. Leaf spot disease of P. odoratum was continuously observed in the Planting Demonstration Garden in Changsha (28 °48 N; 113° 34E), Hunan Province of China, in May 2021 and May 2022. The symptoms initially appeared as tiny reddish-brown spots and continued to expand, resulting in round, oval, or irregular tan lesions with necrotic, film-shaped, or perforated central tissues. Leaf spot disease affects approximately 60-70% of plants. For pathogen isolation, symptomatic leaf samples were collected and disinfected with 70% ethanol for 30 s and 3% sodium hypochlorite for 2 min, followed by rinsing with sterile distilled water. Subsequently, small pieces (3 × 3 mm) of diseased tissues were placed on potato dextrose agar (PDA) and incubated in the dark at 25 °C for 24 h to 36 h. The emerging fungal hyphal tips were transferred to PDA and purified by the single-spore method (Yu, et al., 202). In total, 50 disease spots were isolated, and 10 cultures with the same appearance were obtained. Two strains coded as hnxryzy and hnxryzy01 were randomly selected for identification. After 6 days of culture in PDA, dense pink colonies were observed with a mean radial growth rate of 7.5 mm/day. Strains cultured 6 days on synthetic low nutrient medium, microconidia were oval or ovate (7.5-9.67 µm × 2.49-3.57 µm(n=50)), and macroconidia were sickle-shaped and slightly curved, gradually tapering at both ends, with 2-5 pseudoseptate (10.01-22.14 µm × 2.07-4.22 µm (n=50)). These morphological characteristics were consistent with the description of Fusarium fujikuroi (Fang, et al., 2021). Furthermore, primers ITS1/ITS4, EF728F/EF986R, Bt2a/Bt2b, RPB1-F5/RPB1-R8 and fRPB2-5F2/fRPB2-7cR (Li, et al., 2013, Xie, et al., 2022) were used to amplify the partial region of the internal transcribed spacer (ITS) , the translation elongation factor EF-1α,β-tubulin,polymerase II largest subunit (RPB1) and RNA polymerase II second largest subunit (RPB2) genes from strains hnxryzy and hnxryzy01, respectively. Amplicons were sequenced by Tsingke Biotechnology Co., Ltd. The expected sequences of ITS, EF-1α, β-tubulin, RPB1 and RPB2 of hnxryzy and hnxryzy01 were obtained. The sequence alignment of hnxryzj and hnxryzj01 with the Fusarium ID databased and NCBI shows the following results: The sequences of ITS region, EF-1α, β-tubulin , RPB1 and RPB2 of strain hnxryzy (GenBank accession nos. ON797440, ON820553, ON820554, OP413443, and OP413445, respectively) and strain hnxryzy01 (GenBank accession nos. ON965284, ON968721, ON968722, OP413444, and OP413446, respectively) were 99% to 100% identical to those of F. fujikuroi (GenBank accession numbers CP023090, KC874784, MN490089, MN193916, and MN193888, respectively). Then a phylogenetic tree based on EF-1α, RPB1, and RPB2 sequences was constructed (Torres-Cruz, et al., 2022). The strains hnxryzy and hnxryzy01 were more closely related to F. fujikuroi ( NRRL13566 GenBank accession nos. AF160279, JX171456, and JX171570, respectively), with bootstrap values of 99%. Two sets (5 plants in each set) of potted plants were used in pathogenicity assays. Wounded leaves were sprayed with conidial suspensions (100 µL, 1×107 spores/mL) and sterile water as control. Inoculated plants were covered with plastic bags for 24 h, and maintained at 25 ° C in 12/12 h light/dark conditions in the greenhouse (Yu, et al., 2022). Pathogenicity assays were repeated thrice. Dark brown spots identical to those seen in the field were observed 14 days after inoculation, while the control leaves did not exhibit any symptoms. In this study, the pathogen F. fujikuroi was successfully reisolated from the leaves of inoculated samples showing symptoms, thereby verifying Koch's postulate. To our knowledge, this is the first report of F. fujikuroi inducing leaf spot on P. odoratum in China. Since F. fujikuroi is a common pathogenic fungus that infects different plant species(Qiu, et al., 2020), more attention should be paid to its prevalence in P. odoratum and the potential risk of outbreak in other provinces of China.

Internal Transcribed Spacer Region Typing of Trichophyton interdigitale Isolated from Japanese Patients.

Trichophyton interdigitale, an anthropophilic species, is one of the main causative agents of tinea unguium and tinea pedis. T. interdigitale and the zoophilic species T. mentagrophytes are morphologically and physiologically very similar. Isolates of the T. interdigitale/T. mentagrophytes complex from around the world have been classified into more than 10 internal transcribed spacer (ITS) genotypes. In this study, we isolated T. interdigitale from Japanese patients and investigated which ITS type was more common. The ITS regions of 29 clinical isolates of T. interdigitale and one clinical isolate of T. mentagrophytes were sequenced. The phylogenetic analysis of the ITS region sequences revealed that the 29 isolates of T. interdigitale belong to ITS type II of T. interdigitale. The one clinical isolate of T. mentagrophytes was in the same cluster with ITS type II* of T. mentagrophytes. One terbinafine-resistant strain of T. interdigitale also belonged to ITS type II of T. interdigitale.