Phylogenetic Abnalysis of Malaysian Pineapples Cultivars Based on the DNA Sequence of the Internal Transcribed Spacer Region

The phylogenetic study was conducted to determine the phylogenetic status and evolutionary relationships among the nine commercial pineapple cultivars using sequences of the internal transcribed spacer (ITS) region. Genomic DNA was extracted, and the ITS region was amplified and sequenced. Parsimony analysis revealed that Malaysian cultivars could be classified into two major groups based on the ITS region. The first group comprised of the cultivars Sarawak Green Local, Gandul, and N36 whereas the second group consisted of the cultivars Josapine, Yankee, Morris Bentanggur, Morris Gajah, MD2 and MD2/T. Several combinations of synapomorphic characters (leaf and fruit) support this classification system, suggesting the ITS region has the ability to determine the phylogenetic status and relationships of pineapple cultivars. Since each group has its own similar genetic pattern and presumably certain specific biochemical properties, the relationships of pineapple cultivars revealed in the phylogenetic tree can be used as a basis for successful hybridizations to generate new pineapple cultivars.

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Amanita mansehraensis, a new species in section Vaginatae from Pakistan

Phytotaxa ◽

10.11646/phytotaxa.409.4.1 ◽

2019 ◽

Vol 409 (4) ◽

pp. 189-201 ◽

Cited By ~ 1

Author(s):

MALKA SABA ◽

DANNY HAELEWATERS ◽

MUHAMMAD FIAZ ◽

ABDUL NASIR KHALID ◽

DONALD H. PFISTER

Keyword(s):

New Species ◽

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Large Subunit ◽

Pine Forests ◽

Evolutionary Relationships ◽

Internal Transcribed Spacer Region ◽

Bayesian Inferences ◽

A New Species

A new species of Amanita subgenus Amanita sect. Vaginatae is described and illustrated based on material collected in pine forests in district Mansehra, Khyber Pakhtoonkhaw, Pakistan. Amanita mansehraensis is recognized by the presence of a light brown or light greyish olive pileus with strong brown or deep brown pileus center; non-appendiculate, rimose, sulcate or plicate striate pileus margin; subglobose to ellipsoid basidiospores; and a saccate volva. The internal transcribed spacer region (ITS) and large subunit of the nuclear ribosomal RNA gene (nrLSU) were used for the delimitation of this species based on sequence data. The evolutionary relationships of A. mansehraensis with other species of Amanita were inferred by means of Maximum Likelihood and Bayesian inferences of the nrLSU dataset and concatenated ITS+nrLSU dataset. Amanita mansehraensis is most closely related to A. brunneofuliginea, A. pseudovaginata, and the recently described A. glarea.

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

Journal of AOAC International ◽

10.1093/jaoac/92.5.1464 ◽

2009 ◽

Vol 92 (5) ◽

pp. 1464-1471 ◽

Cited By ~ 21

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.

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Amanita mansehraensis, a new species in section Vaginatae from Pakistan

Phytotaxa ◽

10.11646/phytotaxa.401.3.5 ◽

2019 ◽

Vol 401 (3) ◽

pp. 199

Author(s):

MALKA SABA ◽

DANNY HAELEWATERS ◽

MUHAMMAD FIAZ ◽

ABDUL NASIR KHALID ◽

DONALD H. PFISTER

Keyword(s):

New Species ◽

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Large Subunit ◽

Pine Forests ◽

Evolutionary Relationships ◽

Internal Transcribed Spacer Region ◽

Bayesian Inferences ◽

A New Species

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Evolutionary relationships in Oxytropis species, as estimated from the nuclear ribosomal internal transcribed spacer (ITS) sequences point to multiple expansions into the Arctic

Botany ◽

10.1139/b2012-023 ◽

2012 ◽

Vol 90 (8) ◽

pp. 770-779 ◽

Cited By ~ 11

Author(s):

Annie Archambault ◽

Martina V. Strömvik

Keyword(s):

North American ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Its Region ◽

Its Sequences ◽

The Arctic ◽

Evolutionary Relationships ◽

Data Set ◽

The North ◽

North American Arctic

Species of the genus Oxytropis are distributed in the northern hemisphere, especially in alpine and arctic areas. Although comprehensive taxonomic treatments exist for local floras, an understanding of the evolutionary relationships is lacking for the genus as a whole. To determine if different ancestral Oxytropis species colonized the North American Arctic separately, as suggested by taxonomy, we sequenced the nuclear ribosomal internal transcribed spacer (ITS) region from 16 Oxytropis specimens, including four species that were used in a previous transcriptome study. In addition, 81 other Oxytropis ITS sequences were retrieved from public sequence databases and included in the analysis. The whole data set was analyzed using phylogenetic trees and statistical parsimony networks. Results show that all Oxytropis ITS sequences are very similar. Furthermore, at least six lineages evolved from different temperate ancestors to colonize the North American Arctic. This pattern is believed to be typical of the arctic flora. Additionally, the sequence relationship analyses confirm that the subgenus Phacoxytropis may be ancestral in Oxytropis.

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Parasola psathyrelloides (Psathyrellaceae), a new species from Kerala State, India

Phytotaxa ◽

10.11646/phytotaxa.405.5.4 ◽

2019 ◽

Vol 405 (5) ◽

pp. 255-262

Author(s):

K. G. GREESHMA GANGA ◽

PATINJAREVEETTIL MANIMOHAN

Keyword(s):

New Species ◽

Internal Transcribed Spacer ◽

Large Subunit ◽

Molecular Data ◽

Phylogenetic Study ◽

Internal Transcribed Spacer Region ◽

Comprehensive Description ◽

Morphological And Molecular Data ◽

Kerala State ◽

A New Species

Parasola psathyrelloides sp. nov. is described from Kerala State, India, based on both morphological and molecular data. Comprehensive description, photographs, and comparisons with morphologically similar and phylogenetically related species are provided. Sequences of both the nuclear ribosomal internal transcribed spacer region (ITS) and the nuclear ribosomal large subunit (nLSU) region of the new species were obtained and used in BLASTn searches. The phylogenetic study was based on Maximum likelihood (ML) analysis of the ITS sequences.

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Diagnosing bovine parafilariosis: utility of the cytochrome c oxidase subunit 1 gene and internal transcribed spacer region for PCR detection of Parafilaria bovicola in skin biopsies and serohemorrhagic exudates of cattle

Parasites & Vectors ◽

10.1186/s13071-019-3838-4 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Andreas W. Oehm ◽

Alexander Stoll ◽

Cornelia Silaghi ◽

Annette Pfitzner-Friedrich ◽

Gabriela Knubben-Schweizer ◽

...

Keyword(s):

Internal Transcribed Spacer ◽

Serological Test ◽

Its Region ◽

Effective Control ◽

Intermediate Hosts ◽

Internal Transcribed Spacer Region ◽

Oxidase Subunit ◽

Skin Biopsies ◽

Pcr Targeting ◽

Its Pcr

Abstract Background Parafilaria bovicola (Nematoda: Filariidae) causes cutaneous bleedings in bovine species. Flies serve as intermediate hosts. In recent years, reports on bovine parafilariosis have become more frequent, corroborating the necessity of reliable diagnostic interventions especially since no molecular or serological test has been available. We aimed to establish a polymerase chain reaction assay to detect DNA of P. bovicola in flies, skin biopsies and serohemorraghic exudates of bleeding spots. Methods PCRs targeting the cytochrome c oxidase subunit 1 (cox1) gene and the internal transcribed spacer region (ITS) of the ribosomal RNA gene cluster were evaluated for their diagnostic sensitivity as well as performance and specificity on biopsy and serohemorrhagic exudate samples from P. bovicola-infected cattle. Results Using serohemorrhagic exudates (n = 6), biopsies (n = 2) and flies (n = 1), the PCR targeting the cox1 gene resulted in a gel band of almost 700 bp. Cloning, sequencing, and removal of primer sequences yielded a 649-bp fragment of the P. bovicola cox1 gene. The PCR targeting the ITS region showed a band of about 1100 bp. Cloning, sequencing, and removal of primer sequences resulted in a 1083 bp stretch of the P. bovicola ITS region. Testing samples from presumably affected animals, the cox1-PCR resulted in bands with the expected size and they were all confirmed as P. bovicola by sequencing. In contrast, the ITS-PCR proved to be less sensitive and less specific and additionally amplified the ITS region of Musca domestica or buttercup DNA. When analysing for sensitivity, the cox1-PCR yielded visible bands up to 2 ng of genomic DNA, whereas the ITS-PCR produced bands up to 3 ng. In a plasmid dilution series, the minimum number of target DNA copies was 102 for the cox1-PCR and 101 in the ITS-PCR. Conclusions The evaluated cox1-PCR enables reliable detection of P. bovicola DNA in skin biopsies and serohemorrhagic exudates. This PCR and, to a limited extent, the ITS-PCR, may help evaluate different therapeutic approaches. Furthermore, the cox1-PCR may be useful for epidemiological studies on the geographical distribution of P. bovicola. Further understanding of the epidemiology of this parasite will help develop and implement effective control strategies.

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Phylogeny of Gremmeniella spp. based on sequences of the 5.8S rDNA and internal transcribed spacer region

Canadian Journal of Botany ◽

10.1139/b97-078 ◽

1997 ◽

Vol 75 (5) ◽

pp. 693-698 ◽

Cited By ~ 19

Author(s):

Richard C. Hamelin ◽

Jimmy Rail

Keyword(s):

North American ◽

Internal Transcribed Spacer ◽

Host Specialization ◽

Evolutionary Relationships ◽

Abies Sachalinensis ◽

Internal Transcribed Spacer Region ◽

5.8S Rdna ◽

Asian Race ◽

The North ◽

Distance Methods

Sequences in the 5.8S rDNA and internal transcribed spacer region were obtained for taxa belonging to Gremmeniella spp., and a phylogenetic analysis was carried out using parsimony and distance methods. A set of hypotheses concerning evolutionary relationships between members of that genus was tested. The hypothesis that all members of Gremmeniella abietina var. abietina are closely related was rejected. It appears that the Asian race is quite divergent from the European and North American races, but could be more closely related to G. abietina var. balsamea. The phylogeny was consistent with host specificity: members of G. abietina var. abietina generally do not infect Abies or Picea spp. but the Asian race occurs on Abies sachalinensis in Japan. The hypothesis that host specialization has created divergence within G. abietina var. balsamea was supported by our analysis because the levels of divergence between isolates originating from Picea spp. and Abies spp. were similar to those found between the North American and European races of G. abietina var. abietina. The hypothesis that greater divergence occurred between Gremmeniella abietina and Gremmeniella laricina than between G. abietina var. abietina and G. abietina var. balsamea was not supported. The level of divergence was as large between the two varieties within G. abietina as between the two species G. abietina and G. laricina. These results indicate that similar taxonomic levels should be applied to these three taxa. Key words: scleroderris canker, internal transcribed spacer (ITS).

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Molecular systematics of Keratinophyton: the inclusion of species formerly referred to Chrysosporium and description of four new species

IMA Fungus ◽

10.1186/s43008-021-00070-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Roman Labuda ◽

Andreas Bernreiter ◽

Doris Hochenauer ◽

Alena Kubátová ◽

Hazal Kandemir ◽

...

Keyword(s):

New Species ◽

Internal Transcribed Spacer ◽

Large Subunit ◽

Its Region ◽

Soil Samples ◽

Lsu Rdna ◽

Internal Transcribed Spacer Region ◽

Its Phylogeny ◽

Combined Data ◽

Terminal Cluster

AbstractFour new Keratinophyton species (Ascomycota, Pezizomycotina, Onygenales), K. gollerae, K. lemmensii, K. straussii, and K. wagneri, isolated from soil samples originating from Europe (Austria, Italy, and Slovakia) are described and illustrated. The new taxa are well supported by phylogenetic analysis of the internal transcribed spacer region (ITS) region, the combined data analysis of ITS and the nuclear large subunit (LSU) rDNA, and their phenotype. Based on ITS phylogeny, within the Keratinophyton clade, K. lemmensii is clustered with K. durum, K. hubeiense, K. submersum, and K. siglerae, while K. gollerae, K. straussii and K. wagneri are resolved in a separate terminal cluster. All four new species can be well distinguished from other species in the genus based on phenotype characteristics alone. Ten new combinations are proposed for Chrysosporium species which are resolved in the monophyletic Keratinophyton clade. A new key to the recognized species is provided herein.

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

10.20944/preprints202010.0426.v1 ◽

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.

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Phylogenetic Trees of Aecial-Stage Rust Fungus, Puccinia paederiae (Dietel) Gorlenko Causing Gall on Paederia linearis Hook f.

Walailak Journal of Science and Technology (WJST) ◽

10.48048/wjst.2018.2460 ◽

2017 ◽

Vol 15 (10) ◽

pp. 739-752

Author(s):

Wuttiwat JITJAK ◽

Niwat SANOAMUANG

Keyword(s):

Bayesian Methods ◽

Dna Sequences ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Rust Fungus ◽

Large Subunit ◽

Molecular Data ◽

Small Subunit ◽

Phylogenetic Study ◽

Internal Transcribed Spacer Region

A rust fungus, Puccinia paederiae (Dietel) Gorlenko causing galls on the stem of the skunk vine (Paederia linearis Hook. f. var. linealis and P. linealis var. palida (Craib) Puff) was collected for phylogenetic study as no molecular data was exclusively available for this fungus. Three regions of ribosomal DNA sequences, small subunit (SSU), large subunit (LSU) and internal transcribed spacer region 1 (ITS1) were employed. The results of maximum parsimony and Bayesian methods suggested that among the trees with these sequences, this fungus was nested in Pucciniaceae clades and Puccinia species with supportive statistical values. This is the first report on the phylogenetic analysis using multiple genes of the rust, P. paederiae.

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