Morpho-molecular characterization of Lasiodiplodia theobromae (Pat.) Griffon & Maubl and its first report on the association with coconut kernel from Bangladesh

Pyricularia oryzae tritici, one of the most notorious pathogens of wheat, is a major biotic threat in wheat production around the globe. A total of sixteen P. oryzae tritici isolates isolated from four major wheat blast affected districts viz., Meherpur, Chuadanga, Kustia and Jhenaidaha of Bangladesh were analyzed. Considerable morphological variations in terms of colony color, texture, surface appearance, conidial size and growth pattern were observed. Molecular characterization of the isolates was done based on the sequence information of internal transcribed spacer (ITS) regions. Phylogenetic analysis based on ITS sequences of all the isolates of this study along with 18 reference Pyricularia isolates of different countries (retrieved from NCBI) revealed that isolates belonging to same district of Bangladesh did not form same cluster in the dendrogram. Again, Bangladesh—P. oryzae tritici isolates showed close relationship with other wheat infecting reference isolates from different countries. Isolates infecting other than wheat showed host specific clustering and distantly clustered in the phylogenetic tree. Findings of this study will be helpful for better understanding of this newly evolved pathogen in Bangladesh.

Rhododendron simsii (indoor azalea) is widely cultivated for its high ornamental value (Xu et al. 2021). In April to May 2023, a leaf spot disease occurred in a field study at the Baili Azalea Forest Area (27°12'N, 105°48'E), Guizhou Province, China. About 500 plants were investigated, and the results showed that the incidence of leaf spot was 20 ~ 30%. To study this disease, 10 plants showing severe symptoms were collected. Initially, the symptoms were round or irregularly shaped brown spots (1 to 10 mm). With time, the spots enlarged and merged. Symptomatic leaves were washed with sterile distilled water, and 5 × 5 mm pieces of the infected tissues were removed. After surface sterilization (30 s with 75% ethanol, 2 min with 3% NaOCl, then washed three times with sterilized distilled water), the leaf pieces were dried and placed on potato dextrose agar (PDA) and incubated at 25℃ for 5 days. Fungal colonies developed from leaf tissues, and the germinated spores were transferred onto PDA for further purification and morphological observation. Three isolates (GUBJ23, GUBJ24, and GUBJ12) with similar morphology were obtained from five affected leaves. The representative strain GUBJ23 was selected for further study. On PDA the mycelium was initially white but with sporulation turned gray and then black. Black, single-celled conidia, spherical to sub-spherical, from 11.80 to 21.39 × 13.38 to 21.83 μm (n = 50) in diameter were borne singly on hyaline vesicles at the tips of conidiophores. These morphological characteristics were similar to those of Nigrospora sphaerica (Wang et al. 2017). To confirm the identification, primer pairs for the internal transcribed spacer (ITS) region (ITS5/ITS4), β-tubulin (TUB2) (Bt-2a/Bt-2b), and the translation elongation factor 1-alpha (TEF1-α) (EF1-728F/EF1-986R), were used for PCR amplification of DNA from strain GUBJ23 (Carbone and Kohn 1999; Glass et al. 1995; White et al. 1990). The resulting sequences were deposited in GenBank with accession numbers OR818025 (ITS), OR835150 (TUB2), and OR835147 (TEF1-α). BLAST searches of the sequences revealed 99.80% identity (503/504 bp) of the ITS sequence, 100.00% identity (395/395 bp) of the TUB2 sequence, and 100.00% identity of the TEF1-α sequence (241/241 bp) with N. sphaerica LC7294 (accessions KX985932, KY019602, and KY019397, respectively.) Based on a combined dataset of ITS, TEF1-α, and TUB2 sequences, a phylogenetic tree was constructed using the maximum likelihood method and confirmed that isolates GUBJ23, GUBJ24, and GUBJ12 were N. sphaerica (Wang et al. 2017). Leaves of three healthy R. simsii plants were spray-inoculated with a spore suspension (105 conidia/mL), and an additional three plants were sprayed with sterile water. These plants were incubated at 25℃ in 75% relative humidity. After 5 to 7 days of inoculation, 0.5 to 1.8 mm spots appeared on the leaves. At 10 to 14 days after inoculation, grayish brown, semicircular or irregular lesions appeared on the leaves, usually with a diameter of 0.8 to 3 mm. The symptoms were like symptoms seen on naturally infected leaves, while the control leaves remained asymptomatic. The pathogen was re-isolated from diseased leaves and identified by morphological characterization and molecular analyses (ITS, TUB and TEF1-α), and the reisolated pathogen was identical to N. sphaerica. Thus completing Koch's postulates. According to previous research, N. sphaerica is a widely distributed phytopathogenic fungus that has a wide host range (Wang et al. 2017). This study is the first to identify N. sphaerica as the cause of leaf spot disease in R. simsii. Given the popularity of R. simsii as a pot plant and landscape shrub in Asia and othr regions, the occurrence of leaf spot disease seriously affects its ornamental and economic value. Therefore, it is crucial to establish and implement effective disease management practices to reduce impact of the disease.

More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers?

Species of the genus Colletotrichum are commonly reported as pathogens of fruits in tropical regions. Papaya fruits (Carica papaya L.), cv. Golden, with typical lesions of anthracnose, chocolate spot, and/or stem-end rot were collected from 18 papaya-producing areas of northeast Brazil in 2007. One hundred and fifty-five isolates of Colletotrichum spp. were obtained from the fruit lesions and cultured on potato dextrose agar. Pathogenicity tests were conducted by placing a 20-μl drop of 105 conidia ml-1 suspension on a wounded area of two healthy fruits of cv Golden at the climacteric stage. Inoculated fruits were placed in a moist chamber at 26°C (±2) for 48 h. After this period, the plastic covers of the trays used to form the moist chamber were removed and the trays were kept at 26°C (±2) for 98 h when symptoms were assessed. The causal agents of fruit rot were recovered from inoculated fruits showing symptoms of anthracnose and chocolate spot. Conidia from fresh lesions were collected and measured. Conidia dimensions were 13.49 × 3.80 μm, length/width ratio = 3.55 μm. Conidia were predominantly cylindrical to bluntly rounded ends and slightly flattened. All isolates were morphologically similar to Colletotrichum gloeosporioides Penz (1). Molecular analyses of the isolates were carried out with taxon-specific primers for C. acutatum J.H Simmonds and C. gloeosporioides (3). Only one amplicon was detected for eight isolates with the C. gloeosporioides primer. All isolates were genotyped using inter-simple sequence repeat (ISSR) primers. Three groups of isolates were found, one containing the eight C. gloeosporioides isolates, a second group comprised of 141 isolates, and a third contained six isolates. The second and third groups were more similar to each other than to the first C. gloeosporioides group. Thirty two representative isolates of the three ISSR groups were sequenced for the internal transcribed spacer (ITS) and glutamine synthetase (GS) (GenBank Nos. HM163181 and HM015847) regions. With molecular phylogenetic analyses, two well-supported clades were formed, one with the C. gloeosporioides isolates and the other with sequences highly similar (99% similarity) to the two ITS sequences available in GenBank (DQ003310 and GU358453) and the GS region of G. magna Jenkins & Winstead (DQ792873). The latter was reported in the United States and Taiwan (2,4). Isolates of C. magna and C. gloeosporioides are morphologically similar and identification needs to be based on molecular analyses. To our knowledge, this is the first report of C. magna causing rot of papaya fruit in Brazil.

Preliminary Analysis of the Molecular Phylogenetics of Toxocara canis (Nematoda: Ascaridoidea) Using Nuclear Ribosomal Second Internal Transcribed Spacer Sequences

Objective To profile the intraspecific type of Trichophyton mentagrophytes clinically isolated from different anatomical sites of patients, and to compare the performance of different target sites for the identification of Trichophyton mentagrophytes complex strains. Methods A total of 48 Trichophyton mentagrophytes strains, which were clinically isolated from Department of Dermatology, Wuhan No. 1 Hospital in the latest 3 years, were included in this study. The phenotypes of these Trichophyton mentagrophytes isolates were primarily determined by morphological observation and the urease test. PCR was performed to amplify the nuclear ribosomal internal transcribed spacer (ITS) region and the D1-D2 domains of the large-subunit ribosomal DNA (28S rDNA) followed by DNA sequencing. Then, Clustal X2 software and MEGA 6.0 software were used to analyze the ITS and D1-D2 sequences and to build phylogenetic trees by the maximum-likelihood method (bootstrap= 2000) . Results As the ITS sequence-based phylogenetic tree showed, the probability that the 48 isolates were grouped into the Trichophyton interdigitale clade reached 92%. However, Trichophyton interdigitale could not be effectively differentiated from Trichophyton quinckeanum by the D1-D2 sequence-based phylogenetic tree. In addition, Trichophyton interdigitale showed various appearances, including woolen type, downy type, cream type, powdery type and granular type. Conclusions Trichophyton mentagrophytes can be identified to the species level based on the sequence of ITS region, which shows higher efficiency in identifying Trichophyton mentagrophytes complex than the D1-D2 domains. Morphological characteristics can not serve as the basis for intraspecific typing of Trichophyton mentagrophytes. Key words: Trichophyton; DNA barcoding, taxonomic; DNA, ribosomal spacer; Ribosome subunits, large; Mycological typing techniques

Nai plum (Prunus salicina var. cordata cv. Younai) is one of the most popular fruit crop in South China. In July 2023, a fruit rot of nai plum with about 5 % disease incidence was observed in a fruit market of Changsha city, Hunan Province, China. Initially, small, brown lesions appeared randomly on the fruit surface, with disease progression, the lesions gradually expanded and developed into soft rot. To isolate possible fungi from rotten fruits, small pieces (2 × 2 mm) from the periphery of 10 infected fruits were surface-sterilized using 70% ethanol for 10 s, rinsed three times in sterile distilled water, air dried, and then placed onto potato dextrose agar (PDA) plates and incubated at 28℃ for three days. Emerging colonies were subcultured by hyphal tiptransfer on fresh PDA. A total of ten isolates with similar morphology were obtained. Fungal colonies were initially white, gradually turning gray and eventually becoming black, and aerial hyphae were dense and fluffy. Conidia were hyaline, single celled, ellipsoidal to fusiform, and range from 12.7 to 20.0 μm long (avg. 16.9 ± 2.39 μm) × 5.3 to 7.3 μm wide (avg. 6.3 ± 0.82 μm). These morphological characteristics of these isolates matched those of Neofusicoccum parvum (Phillips et al. 2013). To future confirmation of the identify, the internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (TEF1-a), and beta-tubulin TUB2) genes of two representative isolates (JXNP1 and JXNP2) were amplified and sequenced using primer sets ITS5/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone and Kohn 1999; Phillips et al. 2013), and BT2A/BT2B (Glass and Donaldson 1995), respectively. The sequences of both isolates were deposited in GenBank for the ITS (accession nos. OR899331 and OR899332), TEF1-a gene (accession nos. OR909890 and OR909891) and TUB2 gene (accession nos. OR909892 and OR909893). BLAST analysis showed 99-100% identity with the ex-type strain of N. parvum (CMW9081) for ITS, TEF1-a and TUB2. A maximum likelihood phylogenetic tree was constructed using IQtree web server based on combined ITS, TEF1-a and TUB2 data set. The phylogenetic tree revealed that two isolates clustered with N. parvum in a clade with 90% bootstrap support. Based on morphological and molecular data analysis, the isolates were identified as N. parvum. To confirm the pathogenicity, five healthy nai plum fruits were wounded by using a sterile needle after surface sterilization with 75% ethanol, then a 5-mm-diameter mycelial disc of isolate JXNP1 was taped to the wound, the control fruits were taped with sterile agar plugs. All fruits were incubated at 25 ℃ with 80% humidity. After five days, typical naturally occurring fruit rot symptoms appeared on the fruits which inoculated with N. parvum, whereas control fruits remained asymptomatic. To fulfill Koch's postulates, the pathogen was re-isolated from the inoculated fruits and comfirmed as N. parvum by morphological and molecular analysis. Previous studies reported that N. parvum caused fruit rot on various common fruits in China, including loquat, kiwifruit and citrus (Lei et al. 2013; Zhai et al. 2019; Zhou et al. 2013). To our knowledge, this is the first report of N. parvum causing postharvest fruit rot on nai plum in China. This finding provides critical insights for the management of the high-risk disease on plum in China.

Background: A broad range of diseases affect sorghum which is the major constraint to its production. The most destructive sorghum diseases reported are incited by fungal pathogens, which are widespread globally and result in huge losses in yields both in terms of the quantity and quality of the grains. Aim: The present study identifies the causal agent of Pokkah boeng disease of sorghum in northern Karnataka using a combination of morphological and molecular techniques. Place and Duration of Study: The study was conducted during kharif 2024 in the fields of Main Agricultural Research Station and the Department of Plant Pathology of UAS, Dharwad, Karnataka, India. Methodology: Infected sorghum leaf samples were collected and the pathogen was isolated on potato dextrose agar (PDA). Genomic DNA was isolated for molecular analysis. Morphological observations were taken both macroscopically and microscopically. PCR amplification was done using ITS and TEF primers, and sequenced. A phylogenetic tree was constructed in MEGA software using the sequences obtained for ITS as well as TEF. SDT analysis was also done to understand the identities between the isolates and reference species used. Results: Pathogenicity test confirmed the isolate’s ability to induce disease symptoms in healthy sorghum seedlings, fulfilling Koch’s postulates. The isolate showed white, fluffy growth and had long, curved spores with three septations, as well as oval spores without septations, which are typical features of Fusarium. Molecularly, DNA was extracted, and the internal transcribed spacer (ITS) and translation elongation factor 1-alpha (TEF) regions were sequenced. The obtained sequences of ITS and TEF genes showed 99.75 and 99.81 per cent identity, respectively, to the Fusarium acutatum in the FUSARIOID-ID database, thus confirming the identity. The phylogenetic analysis using the Maximum Likelihood method clustered the isolate with F. acutatum strains, supported by high bootstrap values. Pairwise identity of nucleotide and amino acid sequences of ITS and TEF genes, calculated between the isolate and the reference species. Conclusion: This study marks the first report of F. acutatum as the causal agent of Pokkah boeng disease in sorghum in northern Karnataka, differing from prior reports indicating other Fusarium species.

The genetic relationship of 36 Dendrobium species in China was determined based on sequence analysis of the internal transcribed spacer (ITS) region of ribosomal DNA. Aligned sequences of the complete ITS region obtained from the 36 Dendrobium species and 2 outgroup species (Epigeneium amplum and Epigeneium nakaharaei) by using PCR amplification and direct DNA sequencing. The nrDNA ITS1 of Dendrobium was 225–234 bp and ITS2 was 239–248 bp. Phylogenetic tree was constructed, and seven main clusters were generated among the 36 Dendrobium species. From the results, D. moulmeinense was not grouped in the classification of Dendrobium and E. amplum and E. nakaharaei were shown to be divergent from Dendrobium species. The phylogenetic relationships revealed by ITS DNA analysis partially supported previously published morphological data.

Raillietina species are prevalent in domestic chickens (Gallus gallus domesticus) in Phayao province, northern Thailand. Their infection may cause disease and death, which affects the public health and economic situation in chicken farms. The identification of Raillietina has been based on morphology and molecular analysis. In this study, morphological observations using light (LM) and scanning electron microscopies (SEM) coupled with molecular analysis of the internal transcribed spacer 2 (ITS2) region and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene were employed for precise identification and phylogenetic relationship studies of Raillietina spp. Four Raillietina species, including R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp., were recovered in domestic chickens from 4 districts in Phayao province, Thailand. LM and SEM observations revealed differences in the morphology of the scolex, position of the genital pore, number of eggs per egg capsule, and rostellar opening surface structures in all 4 species. Phylogenetic relationships were found among the phylogenetic trees obtained by the maximum likelihood and distance-based neighbor-joining methods. ITS2 and ND1 sequence data recorded from Raillietina sp. appeared to be monophyletic. The query sequences of R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp. were separated according to the different morphological characters. This study confirmed that morphological studies combined with molecular analyses can differentiate related species within the genus Raillietina in Thailand.

In forensic cases suspected to involve Papaver somniferum, species identification is key to the investigation. To accurately detect and identify P.somniferum as well as common adulterants of the same genus, 19 internal transcribed spacer 2 (ITS2) sequences of P.somniferum (256bp), Papaver canescens (254bp), Papaver nudicaule (254bp), Papaver pavoninum (250bp), Papaver radicatum (254bp), and Papaver rhoeas (256bp) were obtained. Based on the ITS2 sequence, similarity analysis via BLAST, the nearest Kimura-2-parameter (K2P) genetic distances were calculated, and a phylogenetic tree was constructed using MEGA X software for the identification of six species of Papaver. Finally, differences in the ITS2 secondary structure between species were analyzed. The best matches of the P.somniferum ITS2 sequence were of other P.somniferum from different sources. The nearest K2P genetic distances between P.somniferum and its counterparts from other sources were zero, which was the smallest pairwise genetic distance among distances from the other five Papaver species. Various sources of P.somniferum clustered into an independent branch in the phylogenetic tree. The secondary structures of P.somniferum and P.rhoeas were significantly different from those of the other four species of Papaver. In summary, P.somniferum can be effectively distinguished from five closely related plants of the same genus by using ITS2 as a DNA barcode.

Two new species of Lasiodiplodia (Lasiodiplodia endophytica and Lasiodiplodia magnoliae) are described and illustrated from Magnolia forests in Yunnan, China. Endophytic and saprobic Lasiodiplodia pseudotheobromae and endophytic L. thailandica are new records from this host. The internal transcribed spacers (ITS), part of the translation elongation factor-1α (tef1) and partial β-tubulin (tub2) sequence data were analyzed to investigate the phylogenetic relationships of the new species with other Lasiodiplodia species. Lasiodiplodia magnoliae is phylogenetically sister to L. mahajangana and L. pandanicola but morphologically distinct from L. mahajangana in having larger conidia. Lasiodiplodia endophytica is most closely related to L. iraniensis and L. thailandica and the three species can be distinguished from one another by 2 base pair differences in ITS and three or four base pair differences in tef1. The new collections suggest that Magnolia forest plants are good hosts for Lasiodiplodia species with endophytic and saprobic life-styles.

Stem-end rot (SER) causes brown necrotic lesions in the pulp near the base of the fruit pedicel and is one of the most devastating postharvest diseases of avocados in all avocado-growing regions of the world. China's avocado industry is growing very rapidly, and the planting area is expanding, but little is known about the pathogens and genetic diversity of avocado SER. To determine the causal agents of SER, avocado fruits were sampled from the main avocado-producing areas in China during 2020 and 2021. Fungal isolates were obtained from SER symptomatic avocado fruits and identified by morphology combined with phylogenetic analysis of internal transcribed spacer (ITS), translation elongation factor 1-α (EF1-α), and β-tubulin (TUB2) gene sequences. All 101 isolates belonged to Lasiodiplodia spp.; four Lasiodiplodia species were identified, namely, L. pseudotheobromae (59.41%), L. theobromae (24.75%), L. mahajangana (7.92%), and L. euphorbiaceicola (1.98%); and six others are classified as Lasiodiplodia sp. (5.94%). There were only slight morphological differences in colonies and conidia of these four species of Lasiodiplodia. The pathogenicity tests showed symptoms of SER, and 92.08% of the isolates exhibited a high level of virulence on avocado (disease index >70), related to the disease severity on avocado fruits. All tested isolates grew well under the temperature ranging from 23 to 33°C. There was a significant difference in mycelial growth between the four species of Lasiodiplodia after treatment with high or low temperatures. The growth of L. pseudotheobromae was the fastest at 13 to 18°C but was the lowest at 38°C (P < 0.05). The red pigment could be produced by all tested isolates after culturing for 7 days at 38°C. The mycelial growth rate was the fastest on PDA medium, and the slowest on the OMA medium but promoted spore formation (P < 0.05). In addition, the genetic diversity of pathogenic Lasiodiplodia species associated with SER collected from avocado, mango, guava, and soursop fruits was determined. A total of 74 isolates were clustered into four main ISSR groups by the unweighted pair-group method with arithmetic mean analysis, and the classification of this group was related to the host. Extensive diversity was detected in the Lasiodiplodia populations. The diverse geographical origins and host species significantly influenced the population differentiation, and most of the genetic variation occurred within populations (P < 0.001). This is the first study to identify the major pathogens of avocado SER in China, survey their occurrence and pathogenicity, and include a comparative analysis of genetic diversity with Lasiodiplodia spp. causing SER on other fruit hosts. Collectively, the Lasiodiplodia species complex affecting avocado showed high pathogenicity and diversity, while L. pseudotheobromae was the most frequently isolated species in China. The results of this study provide insights into the aspects of the epidemic of SER disease caused by Lasiodiplodia species, which will help in developing strategies for the management and control of SER in avocado.

A new cosmocercid species, Cosmocercoides qingtianensis sp. n., collected from the intestine of the Asiatic toad Bufo gargarizans Cantor (Amphibia: Anura) is described using integrated approaches, including light and scanning electron microscopy, and sequencing and analyzing the ribosomal [small ribosomal DNA (18S) and internal transcribed spacer (ITS)] and mitochondrial [cytochrome c oxidase subunit 1 (cox1)] target regions, respectively. The new species can be distinguished from its congeners by the combination of the following morphological characters, including the large body size, the presence of lateral alae and somatic papillae in both sexes, the length of spicules, the particular morphology and length of gubernaculum, the number, arrangement and morphology of caudal rosettes, the presence of large medioventral precloacal papilla and the long tail. Our molecular analysis revealed the level of intraspecific genetic variation of C. qingtianensis sp. n. distinctly lower than that of the interspecific genetic variation in the ITS and cox1 regions. However, there are some overlaps in the range of intra- and interspecific 18S sequence divergence between the new species and some closely related species. The results of molecular analysis supported the validity of the new species based on the morphological observations. The 18S, ITS, and cox1 regions of C. pulcher collected from Bufo japonicus formosus in Japan were also sequenced and analyzed. The results showed a low level of intraspecific genetic variation in 18S and ITS regions (0-0.12% and 0-0.23% nucleotide differences, respectively), but a relatively high level of intraspecific genetic variation in cox1 region (0.78-4.69% nucleotide differences). In addition, it seems more powerful and practical to use the cox1 region as a genetic marker for the accurate identification and differentiation of species of Cosmocercoides than the 18S and ITS regions, especially for the closely related species.

Phylogenetic Utility of the External Transcribed Spacer (ETS) of 18S–26S rDNA: Congruence of ETS and ITS Trees ofCalycadenia(Compositae)