scholarly journals The UNITE Database for Molecular Identification and for Communicating Fungal Species

2019 ◽  
Vol 3 ◽  
Author(s):  
Urmas Kõljalg ◽  
Kessy Abarenkov ◽  
R. Henrik Nilsson ◽  
Karl-Henrik Larsson ◽  
Andy F.S. Taylor
Keyword(s):  
Molecular Identification ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Fungal Species ◽  
Its Sequences ◽  
Current Version ◽  
Community Members ◽  
Global Biodiversity Information Facility ◽  
Unique System ◽  
Fungal Sequence

UNITE (https://unite.ut.ee; Nilsson et al. 2018) is an international community of scientists and citizen scientists established in 2001. The ambition of UNITE is to develop: 1) datasets and tools for robust and reproducible molecular identification; 2) Persistent Identifiers based system for the communicating fungal species. Datasets of the nuclear ribosomal internal transcribed spacer (ITS) region, form the basis for UNITE. The current version includes nearly 1 million public fungal ITS sequences. Datasets are curated and annotated by community members. During the past 15 years, they made more than 275 000 improvements. In the complete absence of Latin names for species, UNITE offers a unique system where species hypotheses (SH) are provided with Digital Object Identifiers (DOIs). The current version 8 of UNITE offers more than 800 000 DOI-based SHs. One such SH DOI page is shown in Fig. 1. These DOI identifiers are also incorporated into the taxonomic backbone, making communication of taxa seamless in both directions. DOI identifiers of species hypotheses are also used by GBIF (Global Biodiversity Information Facility) in order to publish high-throughput sequencing taxon occurrence data in their data portal. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include ITS-based species hypotheses for all eukaryotes and aggregation of full-length, high-quality ITS sequences generated by the PacBio Sequel system (https://www.pacb.com/products-and-services/sequel-system) from diverse material samples.

scholarly journals PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Elisa Banchi ◽  
Claudio G Ametrano ◽  
Samuele Greco ◽  
David Stanković ◽  
Lucia Muggia ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Computational Effort ◽  
Its Sequences ◽  
Reference Dataset ◽  
Bioinformatic Pipeline ◽  
Taxonomic Level ◽  
Dna Metabarcoding ◽  
Reference Databases

Abstract DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called ‘better clustering for QIIME’ (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.

scholarly journals Microscopic Evaluation, Molecular Identification, Antifungal Susceptibility, and Clinical Outcomes inFusarium,Aspergillusand, Dematiaceous Keratitis

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Devarshi U. Gajjar ◽  
Anuradha K. Pal ◽  
Bharat K. Ghodadra ◽  
Abhay R. Vasavada
Keyword(s):  
Clinical Outcomes ◽  
Amphotericin B ◽  
Molecular Identification ◽  
Antifungal Agents ◽  
Antifungal Susceptibility ◽  
Its Region ◽  
Fungal Species ◽  
Fungal Keratitis ◽  
Accurate Identification ◽  
Microscopic Evaluation

Purpose.Fusarium,Aspergillus, and Dematiaceous are the most common fungal species causing keratitis in tropical countries. Herein we report a prospective study on fungal keratitis caused by these three fungal species.Methodology. A prospective investigation was undertaken to evaluate eyes with presumed fungal keratitis. All the fungal isolates (n=73) obtained from keratitis infections were identified using morphological and microscopic characters. Molecular identification using sequencing of the ITS region and antifungal susceptibility tests using microdilution method were done. The final clinical outcome was evaluated in terms of the time taken for resolution of keratitis and the final visual outcome. The results were analyzed after segregating the cases into three groups, namely,Fusarium,Aspergillus, and Dematiaceous keratitis.Results. Diagnosis of fungal keratitis was established in 73 (35.9%) cases out of 208 cases. The spectra of fungi isolated wereFusariumspp. (26.6%),Aspergillusspp. (21.6%), and Dematiaceous fungi (11.6%). The sequence of the ITS region could identify theFusariumandAspergillusspecies at the species complex level, and the Dematiaceous isolates were accurately identified. Using antifungal agents such as fluconazole, natamycin, amphotericin B, and itraconazole, the minimum inhibitory concentrations (MICs) forFusariumspp. were >32 μg/mL, 4–8 μg/mL, 0.5–1 μg/mL, and >32 μg/mL, respectively. Antifungal susceptibility data showed thatCurvulariaspp. was highly resistant to all the antifungal agents. Overall, natamycin and amphotericin B were found to be the most effective antifungal agents. The comparative clinical outcomes in all cases showed that the healing response in terms of visual acuity of the Dematiaceous group was significantly good when compared with theFusariumandAspergillusgroups (P<0.05). The time required for healing in theFusariumgroup was statistically significantly less when compared with theAspergillusand Dematiaceous groups.Conclusion. This study demonstrates important differences in microscopic features of scraping material and antifungal susceptibility between the three groups. Early and accurate identification coupled with the MIC data, and thereby appropriate treatment is crucial for complete recovery.

scholarly journals The Isolation and Molecular Identification of Bacterial and Fungal Species from Potato Fields of Indore District of Madhya Pradesh

2019 ◽  
Vol 9 (4-s) ◽  
pp. 1207-1209
Author(s):  
Reena Sastiya ◽  
S.M.A. Naqvi ◽  
N.K. Jain
Keyword(s):  
Bacillus Subtilis ◽  
Molecular Identification ◽  
Soil Microorganisms ◽  
Plant Root ◽  
Bacterial Species ◽  
Its Region ◽  
Fungal Species ◽  
Madhya Pradesh ◽  
Healthy Plant ◽  
16S Gene

The microorganisms of rhizosphere play an important role in development of healthy plant. The rhizosphere is the specific fine region of soil that is directly in contact with soil microorganisms and significantly influenced by root secretions. In present study we have studied the microflora of Potato fields of Indore district of Madhya Pradesh. The sampling of soil from rhizosphere using a soil corer with a diameter of 3 cm at a depth of 0–20 cm and sampling of plant root materials as rhizoplane were collected three times: during seedling stage, peak of vegetative growth and fruiting of potato (October/November to February/March) from potato fields of Indore district of Madhya Pradesh. The samples were serial diluted and streaked over the Nutrient Agar and PDA media Plates for the isolation of Bacterial and Fungus. For the identification of Cultured bacterial and fungal species were further analyzed by morphological and Molecular analysis using PCR and sequencing of 16S and ITS region of Bacteria and Fungus species. We reported various types of bacterial (Pseudomonas fluorescens, Pseudomonas aerogenosa, Bacillus subtilis, Pseudomonas putida etc.) and fungal species (Species of Penicillium and Trichoderma etc.) which are required for the development of healthy plant and protection of potato plant from other pathogens. Keywords: Bacterial species, Fungal species, Molecular identification, 16S Gene.

scholarly journals Morphological and molecular identification of four new resupinate species of Lyomyces (Hymenochaetales) from southern China

MycoKeys ◽  
2020 ◽  
Vol 65 ◽  
pp. 101-118
Author(s):  
Jun-Zhu Chen ◽  
Chang-Lin Zhao
Keyword(s):  
New Species ◽  
Molecular Identification ◽  
Internal Transcribed Spacer ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Fungal Species ◽  
Molecular Evidence ◽  
Thin Walled

Four new wood-inhabiting fungal species, Lyomyces bambusinus, L. cremeus, L. macrosporus and L. wuliangshanensis, are proposed based on a combination of morphological and molecular evidence. Lyomyces bambusinus is characterized by resupinate basidiomata with colliculose to tuberculate hymenial surface and broadly ellipsoid, hyaline, slightly thick-walled, smooth basidiospores. Lyomyces cremeus is characterised by resupinate basidiomata with smooth, cream hymenial surface and ellipsoid, hyaline, thin-walled to slightly thick-walled basidiospores. Lyomyces macrosporus is characterized by pruinose basidiomata with reticulate hymenial surface, presence of three kinds of cystidia and larger basidiospores (6.7–8.9 × 4.4–5.4 µm). Lyomyces wuliangshanensis is characterized by coriaceous basidiomata and ellipsoid, hyaline, slightly thick-walled, smooth basidiospores. The phylogenetic analyses based on molecular data of the internal transcribed spacer (ITS) region sequences revealed that the four new species belonged to Lyomyces. Lyomyces bambusinus grouped with L. sambuci. Lyomyces cremeus clade was sister to a clade comprised of L. microfasciculatus. Lyomyces macrosporus was sister to L. allantosporus. Lyomyces wuliangshanensis was closely related to L. mascarensis.

scholarly journals Phylogenetic analysis of Phoma species

2007 ◽  
pp. 100-107
Author(s):  
László Irinyi ◽  
György Kövics ◽  
Erzsébet Sándor
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Elongation Factor ◽  
Its Region ◽  
Morphological Characterization ◽  
Fungal Species ◽  
Its Sequences ◽  
Translation Elongation ◽  
5.8S Rdna

The cosmopolitan Phoma genus contains mainly phytopathogenic, opportunistic parasites, and saprophyte fungal species. Up to now, the characterization of Phoma species and other taxa of Phoma has been determined on the basis of morphology on standardized media, and gene sequence analysis was only used as a confirmative or distinctive complement.In this study, we tried to find molecular markers which can be used as phylogenetics markers in the molecular based classification in the Phoma genus.We employed a part of the translation elongation factor 1 subunit alpha (EF-1α=tef1) containing both introns and exons and ITS region containing the internal transcribed spacer regions 1 and 2 and the 5.8S rDNA, as potential genetic markers to infer phylogenetic relationships among different Phoma taxa. Twelve different Phoma species sequences were analysed together with the closely related Ascochyta ones. The constructed phylogenetic trees, based on tef1 and ITS sequences, do not support the traditional Phoma sections based on morphological characterization. However, we managed to distinguish between the Phoma strains and Ascochyta species by comparing their tef1 sequences through parsimony analysis. We proved that a tef1 can be a useful phylogenetic marker to resolve phylogenetic relationships at species level in Phoma genus.Both parsimony sequence analyses confirmed that the Phyllosticta sojicola species is identical to the Phoma exigua var. exigua species as Kövics et al. (1999) claimed. However, the evolutionary distance by ITS sequences within Phoma species is too small to get well based consequences for the phylogenetic relationships of Phoma genus.Further investigations would be necessary to clarify whether the tef1 and ITS sequences as phylogenetic molecular markers are well suited for the classification of Phoma species.

scholarly journals Problems, Limitations, and Challenges in Species Identification of Ascomycota Members on the Basis of ITS Regions

2020 ◽  
Vol 55 (1) ◽  
Author(s):  
Anna Baturo-Cieśniewska ◽  
Wojciech Pusz ◽  
Katarzyna Patejuk
Keyword(s):  
Species Identification ◽  
Its Region ◽  
Fungal Species ◽  
Plant Diseases ◽  
Its Sequences ◽  
Local Alignment ◽  
Correct Identification ◽  
Rdna Its ◽  
Its Sequence Analysis ◽  
Species Specific

The internal transcribed spacer (ITS) region is regarded as a formal fungal primary barcode with a high probability of the correct identification for a broad group of fungi. ITS sequences have been widely used to determine many fungal species and analysis of rDNA ITS is still one of the most popular tools used in mycology. However, this region is not equally variable in all groups of fungi; therefore, identification may be problematic and result in ambiguous data, especially in some species-rich genera of Ascomycota. For these reasons, identification based on rDNA ITS is usually complemented by morphological observations and analysis of additional genes. Reliable species identification of Ascomycota members is essential in diagnosing plant diseases, verifying air quality and the effectiveness of agronomic practices, or analyzing relationships between microorganisms. Therefore, the present study aimed to verify, using specific examples, the extent to which ITS sequence analysis is useful in species identification of pathogens and saprobionts from Ascomycota and demonstrate problems related to such identification in practice. We analyzed 105 ITS sequences of isolates originating from air and plant material. Basic local alignment search tool (BLASTn) significantly contributed to the reliable species identification of nearly 80% of isolates such as <em>Arthrinium arundinis</em>, <em>Beauveria bassiana</em>, <em>Boeremia exigua</em>, <em>Cladosporium cladosporioides</em>, <em>Epicoccum nigrum</em>, <em>Nigrospora oryzae</em>, <em>Sclerotinia sclerotiorum</em>, or <em>Sordaria fimicola </em>and members of the genera <em>Alternaria </em>and <em>Trichoderma</em>. However, for most isolates, additional morphological observations, information regarding the isolate origin and, where possible, a PCR with species-specific primers were helpful and complementary. Using our practical approach, we determined that ITS-based species identification and comparative analysis with GenBank sequences significantly helps identifying Ascomycota members. However, in many cases, this should be regarded as suggestive of a taxon because the data usually require the use of additional tools to verify the results of such analysis.

scholarly journals Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Wenjun Li ◽  
Xiaofang Li
Keyword(s):  
Community Structure ◽  
Mine Tailings ◽  
Fluorescent In Situ Hybridization ◽  
High Throughput Sequencing ◽  
Microbial Consortia ◽  
Metabolic Reconstruction ◽  
Metal Release ◽  
Community Members ◽  
Oxidative Stresses

Abstract Background Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants’ survival. Results In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion. Conclusions Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.

scholarly journals Morpho-molecular identification and first report of Fusarium equiseti in causing chilli wilt from Kashmir (Northern Himalayas)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ammarah Hami ◽  
Rovidha S. Rasool ◽  
Nisar A. Khan ◽  
Sheikh Mansoor ◽  
Mudasir A. Mir ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Pcr Amplification ◽  
Its Region ◽  
Fungal Species ◽  
Pathogenicity Test ◽  
Kashmir Valley ◽  
Fusarium Equiseti ◽  
Infected Root ◽  
Fusarium Sp ◽  
High Degree

AbstractChilli (Capsicum annuum L.) is one of the most significant vegetable and spice crop. Wilt caused by Fusarium Sp. has emerged as a serious problem in chilli production. Internal transcribed spacer (ITS) region is widely used as a DNA barcoding marker to characterize the diversity and composition of Fusarium communities. ITS regions are heavily used in both molecular methods and ecological studies of fungi, because of its high degree of interspecific variability, conserved primer sites and multiple copy nature in the genome. In the present study we focused on morphological and molecular characterization of pathogen causing chilli wilt. Chilli plants were collected from four districts of Kashmir valley of Himalayan region. Pathogens were isolated from infected root and stem of the plants. Isolated pathogens were subjected to DNA extraction and PCR amplification. The amplified product was sequenced and three different wilt causing fungal isolates were obtained which are reported in the current investigation. In addition to Fusarium oxysporum and Fusarium solani, a new fungal species was found in association with the chilli wilt in Kashmir valley viz., Fusarium equiseti that has never been reported before from this region. The studies were confirmed by pathogenicity test and re-confirmation by DNA barcoding.

scholarly journals In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols

2021 ◽  
Vol 7 (2) ◽  
pp. 99
Author(s):  
Hamza Mbareche ◽  
Marc Veillette ◽  
Guillaume J. Bilodeau
Keyword(s):  
In Silico ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
In Silico Analysis ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Sequence Length ◽  
Universal Method ◽  
Continuous Work ◽  
Its1 And Its2

This paper presents an in silico analysis to assess the current state of the fungal UNITE database in terms of the two eukaryote nuclear ribosomal regions, Internal Transcribed Spacers 1 and 2 (ITS1 and ITS2), used in describing fungal diversity. Microbial diversity is often evaluated with amplicon-based high-throughput sequencing approaches, which is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of the primers used for amplification. The goal of this study is to validate if the mismatches of the primers on the binding sites of the targeted taxa could explain the differences observed when using either ITS1 or ITS2 in describing airborne fungal diversity. Hence, the choice of the pairs of primers for each barcode concur with a study comparing the performance of ITS1 and ITS2 in three occupational environments. The sequence length varied between the amplicons retrieved from the UNITE database using the pair of primers targeting ITS1 and ITS2. However, the database contains an equal number of unidentified taxa from ITS1 and ITS2 regions in the six taxonomic levels employed (phylum, class, order, family, genus, species). The chosen ITS primers showed differences in their ability to amplify fungal sequences from the UNITE database. Eleven taxa consisting of Trichocomaceae, Dothioraceae, Botryosphaeriaceae, Mucorales, Saccharomycetes, Pucciniomycetes, Ophiocordyceps, Microsporidia, Archaeorhizomycetes, Mycenaceae, and Tulasnellaceae showed large variations between the two regions. Note that members of the latter taxa are not all typical fungi found in the air. As no universal method is currently available to cover all the fungal kingdom, continuous work in designing primers, and particularly combining multiple primers targeting the ITS region is the best way to compensate for the biases of each one to get a larger view of the fungal diversity.

scholarly journals Molecular identification of poisonous mushrooms using nuclear ITS region and peptide toxins: a retrospective study on fatal cases in Thailand

2016 ◽  
Vol 41 (1) ◽  
pp. 65-76 ◽  
Author(s):  
Sittiporn Parnmen ◽  
Sujitra Sikaphan ◽  
Siriwan Leudang ◽  
Thitiya Boonpratuang ◽  
Achariya Rangsiruji ◽  
...  
Keyword(s):  
Retrospective Study ◽  
Molecular Identification ◽  
Its Region ◽  
Nuclear Its ◽  
Peptide Toxins ◽  
Poisonous Mushrooms
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