scholarly journals The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253772
Author(s):  
Rosa E. Prahl ◽  
Shahjahan Khan ◽  
Ravinesh C. Deo
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Its Region ◽  
Growth Conditions ◽  
Genetic Distances ◽  
Its Sequences ◽  
Internal Transcribed Spacer Region ◽  
Culture Characteristics

Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.

scholarly journals Molecular Identification of Fusarium Spp. Isolated From Wheat Based on Sequencing of Internal Transcribed Spacer (ITS) Region

2020 ◽  
Author(s):  
Deyana Gencheva ◽  
Georgi Beev
Keyword(s):  
Molecular Identification ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Genetic Distances ◽  
Accurate Information ◽  
Its Sequencing ◽  
Fusarium Spp ◽  
Internal Transcribed Spacer Region ◽  
Genome Region ◽  
Rdna Its

Molecular identification via Internal Transcribed Spacer region (nrDNA-ITS) sequencing of Fusarium spp. isolates from wheat originated from Stara Zagora region, were performed for the first time in Bulgaria. А total of 60 wheat samples (Triticum aestivum) were morphologically identified at the genus level as Fusarium spp. in advance. The rDNA-ITS region of all isolates was successfully amplified and the PCR products obtained were directly sequenced. After a comparison of detected sequences with NCBI database, members of three different fungal genera (Fusarium, Chaetomium, and Alternaria) were identified. Among Fusarium isolates, the F. tricinctum was prevailing, followed by F. poae. A total of three isolate F. proliferatum, F. graminearum and F. equiseti were presented with a single probe. The lowest genetic distance (0.004) was detected between F. tricinctum isolates. On the base of genetic distances, fungal isolates were grouped in two main clusters – one comprising F. tricinctum isolates and F. proliferatum, and second including F. equiseti, F. graminearum and F. poae. It could be concluded that the rDNA-ITS genome region of the genus Fusarium may be used as a suitable marker of early detection, accurate and reliable identification of Fusarium spp. contamination of wheat. The timely and accurate information would assist in the selection of appropriate approaches for control of fusarium infections and possible mycotoxins contamination of agricultural production.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals Application of internal transcribed spacer (ITS) sequences for identifying Anoectochilus setaceus Blume in Thanh Hoa, Vietnam

2020 ◽  
Vol 181 (2) ◽  
pp. 108-116
Author(s):  
B. B. Thinh ◽  
L. D. Chac ◽  
L. T.M. Thu
Keyword(s):  
Internal Transcribed Spacer ◽  
Molecular Taxonomy ◽  
Gene Segment ◽  
Dna Barcode ◽  
Its Sequences ◽  
Gene Region ◽  
Its Gene ◽  
Ctab Method ◽  
Young Leaves ◽  
Total Dna

Background. The term “DNA barcode” is used extensively in molecular taxonomy. Basically, this technique is based on the use of a DNA sequence (about 400–800 bp) as a standard to identify and determine the species relation of organisms quickly and accurately. Therefore, DNA barcodes not only help taxonomists in classifying and identifying species, but also improve their ability to control, understand and utilize biodiversity. In this study, the authors conducted identification of samples of Anoectochilus setaceus Blume collected in Thanh Hoa through the isolated sequence of ITS gene regions.Materials and methods. Total DNA was extracted from young leaves of A. setaceus samples using CTAB method. The ITS gene segment was amplified by PCR and sequenced. This genetic sequence was analyzed, compared and used to establish a phylogenetic tree using BioEdit, BLAST and DNASTAR programs.Results and conclusion. We isolated 4 sequences of the ITS gene region in 4 A. setaceus samples collected at Xuan Lien and Pu Luong of Thanh Hoa province; the ITS gene region was 667 nucleotide long. The findings identified the samples as the same species and showed 99% similarity to the ITS gene sequence of A. roxburghii (Wall.) Lindl. published in GenBank, GQ328774. This study also demonstrates that the method employing internal transcribed spacer (ITS) sequences is an effective tool to identify A. setaceus taxa.

Choiromyces cerebriformis (Tuberaceae), a new hypogeous species from Yunnan, China

Phytotaxa ◽  
2021 ◽  
Vol 482 (3) ◽  
pp. 251-260
Author(s):  
TIAN-JUN YUAN ◽  
OLIVIER RASPÉ ◽  
YONG-JUN LI ◽  
LI WANG ◽  
KAI-MEI SU ◽  
...  
Keyword(s):  
Related Species ◽  
Internal Transcribed Spacer ◽  
Yunnan Province ◽  
Genetic Distances ◽  
Morphological Evidence ◽  
Similar Species ◽  
Sequence Analyses ◽  
Internal Transcribed Spacer Region ◽  
Morphological Differences ◽  
Light Orange

A new hypogeous species, Choiromyces cerebriformis sp. nov. is described and illustrated from Yunnan province, China. Both morphological evidence and sequence analyses of the internal transcribed spacer region (ITS1-5.8S-ITS2) support the species as new to science. C. cerebriformis differs from other Choiromyces species in having ascomata with larger lobes and light orange-brown gleba, and globose ascospores with short stick-like sparse spines ornamentation. Morphological differences and genetic distances with the similar species C. helanshanensis and C. alveolatus are discussed. A phenotypic key including related species is provided.

scholarly journals Database establishment for the secondary fungal DNA barcodetranslational elongation factor 1α(TEF1α)

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 160-169 ◽  
Author(s):  
Wieland Meyer ◽  
Laszlo Irinyi ◽  
Minh Thuy Vi Hoang ◽  
Vincent Robert ◽  
Dea Garcia-Hermoso ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Fungal Infections ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Its Region ◽  
Reference Sequence ◽  
Diagnostic Tools ◽  
Reference Database ◽  
Elongation Factor 1Α ◽  
Fungal Dna

With new or emerging fungal infections, human and animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but it has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode that together with the ISHAM-ITS database, forms the ISHAM barcode database, available online at http://its.mycologylab.org/ . We encourage the mycology community for active contributions.

scholarly journals Qualitative Polymerase Chain Reaction Methods for Detecting Major Food Allergens (Peanut, Soybean, and Wheat) by Using Internal Transcribed Spacer Region

2009 ◽  
Vol 92 (5) ◽  
pp. 1464-1471 ◽  
Author(s):  
Takashi Hirao ◽  
Satoshi Watanabe ◽  
Yusuke Temmei ◽  
Masayuki Hiramoto ◽  
Hisanori Kato
Keyword(s):  
Internal Transcribed Spacer ◽  
Its Region ◽  
Detection Methods ◽  
Target Species ◽  
Internal Transcribed Spacer Region ◽  
Qualitative Polymerase Chain Reaction ◽  
Target Dna ◽  
Allergen Detection ◽  
Specific Amplification ◽  
Polymerase Chain

Abstract Allergen detection methods for peanut, soybean, and wheat were developed by designing PCR primer pairs for specific amplification of a fragment of the internal transcribed spacer (ITS) region reported for Arachis spp. for peanut, Glycine spp. for soybean, and Triticum and Aegilops spp. for wheat. The target species for detection included not only cultivated, but also wild and ancestor species, which were thought to be potentially allergenic. The ability of the resultant primer pairs to detect the target species was verified using genomic DNA extracted from A. hypogaea for peanut and G. max for soybean; T. aestivum, T. turgidum, T. durum, T. aestivum-rye amphidiploid, T. monococcum, T. timopheevi, Ae. speltoides, and Ae. squarrosa for wheat. The LODs were 50500 fg of target DNA, which were comparable to those of the most sensitive PCR methods previously reported. The results from the present work, as well as those from our previous work on buckwheat and kiwifruit, prove that the ITS region, for its high copy number and interspecific diversity, is particularly useful as the target of allergen detection methods.

scholarly journals Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

2012 ◽  
Vol 109 (16) ◽  
pp. 6241-6246 ◽  
Author(s):  
C. L. Schoch ◽  
K. A. Seifert ◽  
S. Huhndorf ◽  
V. Robert ◽  
J. L. Spouge ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Its Region

A molecular phylogeographic study based on DNA sequences from individual metacercariae ofParagonimus mexicanusfrom Guatemala and Ecuador

2003 ◽  
Vol 77 (1) ◽  
pp. 33-38 ◽  
Author(s):  
M. Iwagami ◽  
C. Monroy ◽  
M.A. Rosas ◽  
M.R. Pinto ◽  
A.G. Guevara ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Distinct Species ◽  
Genetic Distances ◽  
Ribosomal Gene ◽  
Chain Reaction ◽  
Geographic Origins ◽  
Polymerase Chain ◽  
Second Internal Transcribed Spacer ◽  
Phylogeographic Study

AbstractA molecular phylogeographic study ofParagonimus mexicanuscollected from Guatemala and Ecuador was performed. Genomic DNA was extracted from individual metacercariae, and two gene regions (partial mitochondrial cytochromecoxidase subunit 1 (CO1) and the second internal transcribed spacer of the nuclear ribosomal gene repeat (ITS2)) were amplified by the polymerase chain reaction (PCR). Sequences segregated in a phylogenetic tree according to their geographic origins. ITS2 sequences from Ecuador and Guatemala differed at only one site. Pairwise distances among CO1 sequences within a country were always lower than between countries. Nevertheless, genetic distances between countries were less than between geographical forms ofP. westermanithat have been suggested to be distinct species. This result suggests that populations from Guatemala and Ecuador are genetically differentiated perhaps at the level of subspecies.

Comparison of the ITS Sequences of 5 Common Potentilla Species in Jilin Province of China

2012 ◽  
Vol 554-556 ◽  
pp. 1690-1693 ◽  
Author(s):  
Shao Xuan Zhang ◽  
Xin Rui Liu ◽  
Bo Chuan Wang ◽  
Yun Hui Ling ◽  
De Jun Sun ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Scientific Data ◽  
Jilin Province ◽  
Its Sequences ◽  
Universal Primers ◽  
Its Sequence ◽  
Its Sequence Analysis ◽  
Pcr Products

To find the differences in the internal transcribed spacer(ITS) sequences and provide scientific data for the authentication of Potentilla chinensis and its related species, we extracted the genome DNA from the leaves of 5 common Potetilla species in Jilin Province, amplified the ITS region using ITS universal primers of angiosperm, and sequenced the purified PCR products directly. Polymorphism of ITS sequences was found within P. chinensis and the sequence data suggested that our samples of this species might be related to hybridization. Other 4 species showed intraspecies-stability in ITS sequence. The ITS sequences of these 5 Potentilla species are significantly different. So ITS sequence analysis and other methods derived from it can be used in authentication of Potentilla.

scholarly journals Amanita pseudovaginata from Pakistan

2020 ◽  
Vol 5 (3) ◽  
pp. 19
Author(s):  
Abdul Nasir Khalid ◽  
Arooj Naseer
Keyword(s):  
Molecular Analysis ◽  
Fruiting Body ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Its Sequences ◽  
Published Data ◽  
Fungal Symbiont ◽  
Internal Transcribed Spacer Region ◽  
First Report ◽  
Quercus Spp

Amanita pseudovaginata of Amanita subgenus Amanita sect. Vaginatae was found associated with Quercus spp. forests during a survey of macrofungi from oaks forests of Pakistan. The fruiting body was characterized morphoanatomically as well as by molecular analysis. The identification of the fungal symbiont as Amanita pseudovaginata was confirmed by Internal Transcribed Spacer Region (ITS) sequences. Sporocarps were matched with published data available from Russia and China. Phylogenetic analyses and morphological descriptions are provided. This represents the first report of this species in Pakistan.

Sign in / Sign up

Export Citation Format

Share Document