Search Results (228)

Background: Rosa L. is an economically significant genus with species that are notable for their rich content of phenolic compounds. Despite its importance, the taxonomy of Rosa remains complex and unresolved. Methods: We sequenced, assembled, and performed comparative analyses of the complete plastomes of four Rosa species: R. acicularis, R. iliensis, R. laxa, and R. spinosissima. In addition to the plastome, we sequenced the nuclear ribosomal internal transcribed spacer (ITS). Results: Plastomes ranged in size from 157,148 bp (R. iliensis) to 157,346 bp (R. laxa). In each plastome, 136 genes were annotated, comprising 90 protein-coding, 38 tRNA, and eight rRNA genes. A total of 905 SSRs were identified, ranging from 224 (R. acicularis) to 229 in R. spinosissima. Nine highly variable regions were detected, including two coding genes (rps16 and ycf1) and seven intergenic spacers (ycf3-trnS(GGA), trnT(UGU)-trnL(UAA), rpl14-rpl16, trnR(UCU)-atpA, trnD(GUC), trnG(UCC)-trnfM(CAU), and psbE-petL). Maximum Likelihood (ML) phylogenetic analyses based on the complete plastome and ycf1 gene datasets consistently resolved the Rosa species into three major clades, with strong bootstrap support. In contrast, the ML tree based on ITS resolved species into four clades but showed lower bootstrap values, indicating reduced resolution compared to plastid datasets. Conclusions: Our findings underscore the value of plastome data in resolving phylogenetic relationships within the genus Rosa. Full article

With 493 taxa and 63 sections, Astragalus L. is the largest genus in Türkiye. Most of these are narrow endemics and usually found in marginal habitats or require edaphic specializations (about 42% of the species are endemic). Due to the genus’s extensive diversity of species and common economic use, numerous scientific studies have concentrated on specific species. Taxonomic categorization based on morphological characteristics is insufficient to distinguish certain taxonomic groups. However, there is no systematic molecular phylogenetic analysis of Turkish species that deals with speciation in this genus. To concentrate on molecular-level speciation, fresh leaves from 152 samples representing 30 species across six sections native to Türkiye were collected over several months of comprehensive field studies and analyzed with regard to the internal transcribed spacer (ITS) of nrDNA and the trn L5′-L3′ + L3′-F(GAA) + mat K of cpDNA regions. Additionally, molecular clock estimations and biogeographical histories were analyzed to clearly understand the species’ divergence. Based on all studied regions, the Poterion section was found to be the newest and most divergent section, while the Megalocystis Bunge and Halicacabus Bunge sections were the closest and older ones. Furthermore, A. vaginans from section Hymenocoleus Bunge were included not only in this section but also in several other lineages. It is noteworthy that A. dipodurus and A. oleaefolius species from the section Macrophyllium Bunge are usually put together in a distinct sub-branch from other species members of the section in phylogenetic trees generated using both researched cpDNA and nrDNA regions. Moreover, some of the species are divided by the Anatolian diagonal, and the speciation of a significant number of species began during the Pleistocene geological time period. Geographical isolations or other weak isolation mechanisms preceded speciation in Astragalus, which requires more research in the future. Full article

The Antarctic continent hosts highly specialized microbial ecosystems, particularly within endolithic habitats, where microorganisms colonize the interior of rocks in order to withstand conditions that otherwise cannot support life. Previous studies have characterized the composition and abundance of these communities, as well as their different degrees of stress power; furthermore, the effect of different lithic substrates in shaping their associated bacterial assemblages has been extensively investigated. By contrast, how rock typology exerts fungal endolithic colonization still remains unexplored. In this study, we have considered and compared fungal communities inhabiting granite and sandstone rocks collected across Victoria Land, Antarctica, using high-throughput sequencing of the Internal Transcribed Spacer (ITS) region. Our analyses revealed that both rock types were dominated by Ascomycota, with a marked prevalence of lichen-forming fungi, particularly within the class Lecanoromycetes. However, granite-supported communities exhibited significantly higher species richness, likely driven by the structural heterogeneity of the substrate and the presence of fissures enabling chasmoendolithic colonization. In contrast, sandstone communities were more specialized and dominated by strict cryptoendolithic taxa capable of surviving within the rock’s pore spaces. Differential abundance analysis identified key species associated with each substrate, including the lichen Buellia frigida in granite and the black fungus Friedmanniomyces endolithicus in sandstone, two endemic species in Antarctica. Moreover, the use of presence/absence- versus abundance-based diversity metrics revealed contrasting ecological patterns; substrate type had a stronger influence on species presence, whereas geographic location more significantly shaped abundance profiles, highlighting the complex interplay between both factors in determining fungal community composition. Additionally, alpha diversity analyses showed significantly higher species richness in granite compared to sandstone, suggesting that structural heterogeneity and chasmoendolithism may promote a more diverse fungal assemblage. Full article

Biosecurity is vital to Australia’s efforts to prevent and respond to pests and diseases. Here, we report on testing suspected illegal goods (SIGs) as part of an active Australian biosecurity response in Sydney. The Australian Government, Department of Agriculture, Fisheries and Forestry detected and secured consignments containing tuber products of unknown biosecurity risk and origin. Swab samples were collected from vacuum-sealed yam products, organic packing material (background negative controls), and field negative controls to assess possible cross-contamination from the storage facility. DNA from all samples was analysed using high-throughput metabarcoding targeting the Internal Transcribed Spacer 2 (ITS2) and the chloroplast trnL (UAA) P6 Loop gene regions by two independent teams in Australia. A plant community profile comprising Australian native species and other non-native established species would support the notion of produce being harvested and/or packaged domestically, while their absence would suggest foreign production. Of the 5,764,942 total reads produced, the bioinformatic analysis generated 5,181,530 amplicon sequencing variants employed for species identification. Twenty plant taxa were identified via ITS2 and 15 via trnL, corresponding to worldwide distributed plants, non-native species established in Australia, or species not recorded in Australia. No Australian endemic species were detected. The absence of common Australian native plants, combined with the presence of species not known to occur in Australia, provided strong evidence that the suspect tuber products were illegally imported. Full article

Dollar spot is one of the world’s most widely distributed turfgrass diseases. The pathogen of the disease has been re-identified as a fungus belonging to the genus Clarireedia in the United States, Japan, and China. Since Clarireedia species vary depending on the response to fungicides, hosts, and distribution ranges, it is necessary to re-identify dollar spot in South Korea for effective turfgrass management. In this study, the amplified nucleotide sequences with primer sets of the internal transcribed spacer (ITS) region, Calmodulin (CaM), and Mini-chromosome maintenance complex component 7 (Mcm7) were analyzed to re-identify Clarireedia spp. isolated from creeping bentgrass and Kentucky bluegrass on golf courses in South Korea. The ITS and CaM regions were analyzed through multiple sequence alignments. The isolates were identified as C. paspali, and Clarireedia sp. When cultured on PDA, three groups formed fast growing, cottony colonies with white aerial hyphae that later collapsed and turned tan to brown. Most isolates formed apothecia, but ascospores were not observed. The apothecia formation of C. paspali has never been reported. All isolates exhibited pathogenicity on creeping bentgrass and Kentucky bluegrass. These results indicated that the pathogens causing dollar spot on creeping bentgrass and Kentucky bluegrass in South Korea might be C. paspali and Clarireedia sp. The present study reports the first re-identification of the turfgrass dollar spot pathogen Sclerotinia homoeocarpa into the genus Clarireedia in South Korea. Full article

The order Pezizales (Ascomycota) consists of cup and truffle fungi growing in a wide range of habitats and geographical zones worldwide, exhibiting diverse nutritional behaviors. In Israel, morphological studies have designated most Pezizales as saprotrophs. We re-screened Pezizales mushrooms collected in northern Israel between 2020–2022 using molecular tools based on DNA sequences of partial large subunit rRNA (28S), internal transcribed spacer (ITS), and partial heat shock protein (Hsp90) regions, along with macro images of each freshly collected samples. Trophic mode was determined through available literature and δ¹³C and δ¹⁵N stable isotope analysis along with a quadratic discriminator analysis (QDA) model to predict trophic modes: 112 collections were positively identified with identification of 23 genera; 23 taxa were resolved to the species level, 11 to approximate species, and 15 to the genus level. Helvella was the most species-rich genus; 25 species and species approximations were newly reported for Israel. Further molecular phylogenetic studies are needed to resolve species identity of the Israeli Pezizales. Most Pezizales collections were determined by trophic mode studies to be ectomycorrhizal, with a few saprotrophs. The QDA model yielded several samples with undefined nutritional behavior or a different trophic mode than previously inferred, suggesting that more in-depth study is needed to understand their trophic ecology. This study improves knowledge regarding species diversity, ecology, and evolution of Israeli Pezizales. Full article

The possible origin of four cultivated species of the genus Avena of different ploidy and different subgenome composition (A. strigosa, A. abyssinica, A. byzantina, and A. sativa) from possible wild species was investigated. The region of the internal transcribed spacer ITS1 and the 5.8S rRNA gene in the cultivated species was studied with next-generation sequencing (NGS), and the patterns of occurrence and distribution of the ribotypes were compared among them and with those of the wild species. According to these data diploid, A. strigosa is more closely related to the diploid A. hirtula than to polyploid oats, and it could have evolved independently of polyploid cultivated species. The tetraploid Avena abyssinica could be a cultivated derivative of A. vaviloviana. Two hexaploid cultivated species, A. byzantina and A. sativa, could have a different origin; A. sativa could be the cultivated form of A. fatua, whereas A. byzantina could originate independently. It was found that the oat species with the A and C subgenomes, even with strong morphological and karyological differences, could intercross and pass the further stages of introgression producing a new stable combination of genomes. Our data show that almost all species of Avena could form an introgressive interspecies complex. Full article

Cutaneous leishmaniasis (CL) is a significant public health concern that affects many countries. This disease is caused by the protozoan parasite Leishmania spp. and is transmitted through the sandflies from the genus Phlebotomus and Lutzomyia. The clinical manifestations of CL can vary, often leading to challenges in accurate diagnosis and treatment. In 2022, a 51-year-old male patient presented to a tertiary care hospital in Puducherry, India, with progressively worsening facial lesions and granulomatous plaques. The patient had recently returned from Saudi Arabia, where he likely contracted the infection. Before he visited the tertiary care hospital in Puducherry, the patient had been misdiagnosed and treated for conditions such as Erysipelas and Acute Cutaneous Lupus Erythematosus (ACLE), highlighting the diagnostic challenges associated with CL. Skin scrapings from the patient were subjected to real-time PCR, confirming Leishmania spp.’s presence. Cytological examinations revealed the amastigote-like structures within macrophages, thereby establishing the identity of the parasite. For precise species-level identification, PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) and Sanger sequencing of the Internal Transcribed Spacer-1 (ITS-1) region were performed. Molecular techniques confirmed the infection as being caused by Leishmania tropica. Following the accurate diagnosis, the patient was successfully treated with Liposomal Amphotericin B, a treatment known for its efficacy against Leishmania infections. This case underscores the critical importance of considering cutaneous leishmaniasis in the differential diagnosis of travelers returning from endemic areas who present with dermatological manifestations. The initial misdiagnosis and inappropriate treatment highlight the need for heightened clinical awareness and the utilization of advanced diagnostic tools for accurate identification. Effective and timely treatment, as demonstrated in this case, is essential for the management and control of the disease. This report emphasizes the necessity of vigilance among healthcare providers to recognize and appropriately address imported cases of cutaneous leishmaniasis. Full article

The fungal family Botryosphaeriaceae, which includes genera such as Diplodia, Dothiorella, and Phaeobotryon, comprises species commonly associated with woody plants such as endophytes, pathogens, and saprophytes. The Xizang Autonomous Region of China, known for its rich forest resources, harbors significant fungal diversity. However, limited research has been conducted on plant-disease-associated fungi in this region. In this study, we employed morphological characteristics and molecular phylogenetic analyses of the internal transcribed spacer region of rDNA (ITS), the ribosomal large subunit (LSU), the translation elongation factor 1-alpha (tef1) gene, and the partial beta-tubulin (tub2) gene to identify fungal species. As a result, two new species, Diplodia salicicola sp. nov. and Phaeobotryon xizangense sp. nov., are proposed and described herein. Additionally, Di. corticola, Di. mutila, Do. acericola, Do. magnoliae, Do. vidmadera, Do. yunnana comb. nov., and Do. zanthoxyli are reported for the first time in Xizang. Our findings contribute to advancing the knowledge of fungal biodiversity in Xizang’s high-altitude ecosystems. Full article

Sargassum hemiphyllum var. chinense is a common brown seaweed along the southeastern coast of China, playing a significant ecological role and possessing considerable resource utilization value. However, its genetic diversity and phylogeographic patterns remain poorly understood. In this study, we employed multiple molecular markers, including the nuclear ITS sequence (ribosomal internal transcribed spacer), the plastid rbcL gene (encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase), and the mitochondrial cox3 and cox1 genes (encoding cytochrome c oxidase subunits III and I, respectively), to elucidate the genetic and phylogeographic structure of S. hemiphyllum var. chinense. Our findings demonstrate that the combined use of plastid and mitochondrial gene sequences is suitable for phylogeographic studies of this species. Genetic structure difference was observed among 15 populations which localities covering most of its distribution range, likely resulting from colonization by ancestors of different origins and limited gene flow among populations. The study revealed two distinct lineages of S. hemiphyllum var. chinense, exhibiting a north–south geographical distribution with a mixed zone in the southern Fujian–eastern Guangdong coastal region. These lineages are inferred to have diverged during the Middle to Late Pleistocene due to the isolation of the East China Sea and South China Sea during glacial periods. Sub-lineage differentiation was also detected within the northern lineage. The southern lineage experienced demographic expansion following the end of the Last Glacial Maximum, while the northern lineage remained stable. The southern Fujian–eastern Guangdong region, characterized by high genetic diversity, may have served as a glacial refugium or a contact zone for the post-glacial recolonization of the two lineages. Global warming may lead to range contraction and reduced genetic diversity in this species. The high genetic diversity area should be prioritized for conservation efforts. Overall, these findings provide insights into the genetic structure status and causes of S. hemiphyllum var. chinense and offer a scientific basis for proposing reasonable measures for its resource management. Full article

Hypocreales is one of the largest orders within the class Sordariomycetes and is renowned for its diversity of lifestyles, encompassing plant, insect, and human pathogens, as well as endophytes, parasites, and saprobes. In this study, we focused on saprobic hypocrealean fungi isolated from rice in northern Thailand. Species identification was conducted using morphological characteristics and multilocus phylogenetic analyses, including the internal transcribed spacer region (ITS), 28S large subunit nuclear ribosomal DNA (LSU), translation elongation factor 1–alpha (tef1-α), RNA polymerase II second-largest subunit (rpb2), and calmodulin (cmdA). This research confirmed the presence of 14 species of hypocrealean taxa, viz. Fusarium (9), Ochronectria (1), Sarocladium (2), Trichothecium (1), and Waltergamsia (1). Among these were two new species (Fusarium chiangraiense and F. oryzigenum), four new host records (Fusarium kotabaruense, Ochronectria thailandica, Sarocladium bactrocephalum, and Waltergamsia fusidioides), and three new geographical records (Fusarium commune, F. guilinense, and F. hainanese). Full article

Background: Anopheles stephensi, a primary malaria vector in South Asia, is expanding its geographic range, raising concerns about increased malaria transmission. However, critical aspects of its genetic diversity, population structure, and evolutionary dynamics remain poorly understood in Khyber Pakhtunkhwa (KP), Pakistan, an endemic malaria region where An. stephensi is adapting to urban settings, posing challenges for the development of targeted vector control strategies. This study addresses this gap by analyzing COI, COII (cytochrome oxidase subunit I and II), and ITS2 (internal transcribed spacer 2) sequences from An. stephensi populations in KP and comparing them with global isolates. Additionally, egg morphology analysis was conducted to identify the biological form. Methods: Mosquitoes were collected from malaria-endemic districts (Nowshera, Charsadda, and Peshawar) using ovitraps. Eggs were characterized morphologically, and DNA was extracted for PCR amplification of COI, COII, and ITS2 markers. Sequences from 17 Pakistani isolates, along with global sequences, were analyzed. Phylogenetic relationships, haplotype networks, genetic diversity, and neutrality tests (Tajima’s D and Fu’s Fs) were assessed. Results: Egg morphology confirmed the mysorensis form (13–15 ridges per egg) in KP. COI sequences clustered into two subclades (Punjab and KP), with >99% similarity to global isolates. COII and ITS2 sequences showed high similarity (99.46–100%) with populations from China, Iran, India, and Brazil, reflecting strong genetic connectivity rather than distinct regional clustering. Haplotype analysis identified six COI, ten COII, and ten ITS2 haplotypes, with Hap_2 (50.7%) and Hap_1 (43.3%) being the most prevalent in COI, Hap_7 (29.4%) in COII, and Hap_3 (80.8%) in ITS2. Population genetic analysis revealed higher COI diversity in Pakistan and India, with moderate diversity in COII. Neutrality tests suggested balancing selection in COI for both countries, while COII and ITS2 indicated population contraction in Iran. Conclusions: The findings reveal strong genetic connectivity within regions (e.g., Pakistan) and differentiation across global populations of An. stephensi, highlighting its potential for further expansion and adaptation. These insights are critical for informing global malaria control strategies, particularly in regions vulnerable to vector invasion. Full article

Recently, Fusarium root rot (FRR)-like symptoms were observed in Uganda’s agroecology zones, prompting the National Agricultural Organisation (NARO) to conduct a disease survey. The survey reports indicated FRR as the second most prevalent root rot disease of common bean in Uganda after Southern blight. Ninety nine Fusarium spp. strains were obtained from samples collected during the surveys. The strains were morphologically and pathogenically characterised and confirmed to cause Fusarium root rot as observed in the field. However, molecular characterization of the strains was not conducted. In this study, therefore, 80 of the strains were characterized using partial sequences of translation elongation factor 1-alpha (TEF-1α) gene, beta tubulin (β tubulin) gene and internal transcribed spacers (ITS) region of ribosomal RNA to determine species diversity. High-quality Sanger sequences from the target genes were compared to the sequences from Fusarium species available in the National Centre for Biotechnology Information coding sequences (NCBI-CDS) database to determine the most likely species the strains belonged. The sequences from our strains were deposited into the NCBI gene bank under ID#288420, 2883276, 2873058 for TEF-1α, β tubulin and ITS respectively. The Fusarium species identified included; F. oxysporum, F. solani, F. equiseti F. delphinoides, F. commune, F. subflagellisporum, F. fabacearum, F. falciforme, F. brevicaudatum, F. serpentimum, F. fredkrugeri and F. brachygibbosum. The diversity of these Fusarium species needs to be taken into consideration when developing breeding programs for management of the disease since currently there is no variety of common bean resistant to FRR in Uganda. Full article

In recent years, Castanopsis carlesii, a keystone species in southern China’s forest ecosystems with high ecological and economic importance, has faced growing challenges from severe nut rot diseases. Gnomoniopsis (Gnomoniaceae, Diaporthales, Sordariomycetes, Ascomycota) represents a significant fungal genus that causes leaf spots, branch cankers, and fruit rot diseases. In this study, rotten nuts of C. carlesii were collected from Fujian Province, and fungal isolates were obtained using the tissue isolation method. Morphological characterization and molecular phylogenetic analysis, based on the combined sequences of the internal transcribed spacer region of rDNA (ITS), the translation elongation factor 1-alpha (tef1) gene, and the partial beta-tubulin (tub2) gene were used to identify these isolates. As a result, new isolates from diseased nuts of C. carlesii formed a distinct clade with Gnomoniopsis, and morphologically differentiated from the other species; hence, G. flava sp. nov. is proposed herein. Furthermore, pathogenicity tests involving three isolates of G. flava were conducted on healthy nuts of C. carlesii, confirming its role as the causal agent of this new plant disease. This study not only advances our understanding of species diversity within Gnomoniopsis but also lays the groundwork for developing control strategies for C. carlesii nut rot disease. Full article

Fungal endophytes of medicinal plants produce diverse secondary metabolites and extracellular enzymes with therapeutic and biotechnological potential. However, the biological and biotechnological potential of fungal endophytes from South African medicinal plants remain relatively underexplored. In this study, the antimicrobial, antioxidant, anti-inflammatory and extracellular enzymatic capabilities of five fungal endophytes previously isolated from the leaves of Kirkia acuminata Oliv. were investigated. Sequencing of the internal transcribed spacer (ITS) regions revealed that the isolates belonged to the genera Setosphaeria, Diaporthe and Corynespora. The broth micro-dilution assay and the Folin–Ciocalteau reagent method were used to assess the antibacterial activity and the total phenolic content (TPC) of the fungal endophytes’ ethyl acetate crude extracts (CEs), respectively. The antioxidant activity was assessed using the ferric reducing antioxidant power (FRAP) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging assays. The influence of the CE of the Setosphaeria rostrata KaL-4 on the viability and LPS-induced interleukin-6 (IL-6) production in Raw 264.7 macrophages was assessed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and an ELISA, respectively. The ability of the isolates to produce extracellular proteases, laccases and peroxidases was also determined. The CEs displayed antimicrobial activity with MICs ranging from 0.63 to 1.25 mg/mL and reducing power and scavenging activity ranging from 40% to 18% and from 60% to 48%, respectively. The S. rostrata KaL-4 CE possessed the highest TPC and demonstrated dose-dependent cytotoxicity. The CE further demonstrated a significant reduction in IL-6 production at a concentration of 0.75 µg/mL. Only one isolate demonstrated the ability to produce proteases with an enzymatic index (EI) of 0.66, while laccases (EI range of 0.14 to 1.15) and peroxidases were produced by all of the isolates. These findings suggest that fungal endophytes from South African medicinal plants are promising sources of bioactive compounds and industry-significant extracellular enzymes. Full article