scholarly journals rDNA based analysis of autochtonous fungal species from Serbia

Genetika ◽  
2014 ◽  
Vol 46 (1) ◽  
pp. 33-42
Author(s):  
Eleonora Capelja ◽  
Nevena Stevic ◽  
Vladislava Galovic ◽  
Milana Novakovic ◽  
Maja Karaman
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Data ◽  
Fungal Species ◽  
Its Sequences ◽  
Local Alignment ◽  
Phylogenetic Species Concept ◽  
Morphological Approach ◽  
Search Tool ◽  
Morphological And Molecular Data

Determination of fungal species by traditional morphological approach can often be problematic. In the phylum Basidiomycota, sporocarps of different species can share very similar morphoanatomical characteristics. Using molecular markers and phylogenetic species concept this problem can be reduced. In this study identification of six autochtonous fungal species, collected from several locations in Serbia (Tara, Kopaonik, Stara planina) was done by comparison between morphological and molecular data of fungal species, as well as information obtained from phylogenetic tree. ITS sequences amplified from 11 specimens of two genera of ph. Basidiomycota: Marasmius and Ganoderma, were compared with ITS sequences from database using basic local alignment search tool (BLAST). Phylogenetic tree was constructed using Neighbor joining method based on differences between analyzed ITS sequences. Our results showed that within genera Marasmius and Ganoderma morphological and molecular determinations are usually in accordance, but for proper species delimitation both approaches should be used.

scholarly journals Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

2021 ◽  
Vol 322 ◽  
pp. 01038
Author(s):  
Tuah N. M. Wulandari
Keyword(s):  
Phylogenetic Tree ◽  
Coi Gene ◽  
Local Alignment ◽  
Mtdna Sequences ◽  
Mitochondrial Coi ◽  
Search Tool ◽  
Very High ◽  
I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

Genotyping of Acanthamoeba Species Isolated from Keratitis Patients by PCR Sequencing Methods in Tehran, Iran

2019 ◽  
Author(s):  
Tooran Nayeri Chegeni ◽  
Fatemeh Ghaffarifar ◽  
Majid Pirestani ◽  
Fariba Khoshzaban ◽  
Abdolhosein Dalimi Asl ◽  
...  
Keyword(s):  
Contact Lenses ◽  
Pcr Amplification ◽  
Acanthamoeba Keratitis ◽  
Local Alignment ◽  
Sequencing Analysis ◽  
Search Tool ◽  
Skin Nodules ◽  
Acanthamoeba Species ◽  
Eye Clinic

  Background and Aims: Amoebae of the genus Acanthamoeba are unicellular amphizoic opportunistic pathogens that may cause fatal granulomatous encephalitis, eye keratitis, amebic pneumonitis and skin nodules as well as abscesses in humans and animals. Acanthamoeba keratitis is caused by trauma to the eye, contaminated cleaning solutions and the use of contact lenses. The aim of the present study was to identify the genotypes of Acanthamoeba in all patients with a clinical diagnosis of Acanthamoeba keratitis referring to eye clinic in Tehran using polymerase chain reaction (PCR).  Materials and Methods: In this study, samples were collected from 35 patients who had referred to the eye clinic and were cultured on 1.5% non-nutrient agar. DNA was extracted, and then PCR amplification was performed using genus specific primers. Sequencing analysis and basic local alignment search tool search were conducted to determine the genotypes. Phylogenetic tree was generated using maximum likely algorithm in phylogenetic program MEGA version 6.  Results: Eight cases were positive for Acanthamoeba using genus specific primer pairs. All specimens were reported as genotype T4. Conclusions: Determination of genotypes showed all isolates belonging to genotype T4; this abundance may be due to its higher prevalence in the environment or its greater virulence. However, further analysis of clinical and environmental samples is necessary to clarify this property.   

The Philodromus pulchellus-group in the Mediterranean: taxonomic revision, phylogenetic analysis and biogeography (Araneae:Philodromidae)

2007 ◽  
Vol 21 (1) ◽  
pp. 39 ◽  
Author(s):  
Christoph Muster ◽  
Robert Bosmans ◽  
Konrad Thaler
Keyword(s):  
Taxonomic Revision ◽  
Molecular Data ◽  
Species Group ◽  
Western Mediterranean ◽  
Mediterranean Origin ◽  
Character Variation ◽  
Nomina Dubia ◽  
Morphological And Molecular Data ◽  
Continuous Character

The Philodromus pulchellus species-group is defined and diagnosed. Eleven species are included, described or redescribed, keyed and illustrated: P. afroglaucinus, sp. nov. from Algeria; P. bistigma Simon, 1870, P. glaucinus Simon, 1870, P. lamellipalpis, sp. nov. from Algeria; P. medius O. P.-Cambridge, 1872; P. pardalis, sp. nov. from northern Africa and the Iberian peninsula; P. pulchellus Lucas, 1846, P. punctigerus O. P.-Cambridge, 1908, P. ruficapillus Simon, 1885, P. simoni de Mello-Leitão, 1929, and P. wunderlichi, sp. nov. from the western Canary Islands. The validity of P. bistigma and P. medius is re-established (formerly in synonymy with P. pulchellus); neotype and lectotype, respectively are newly designated. The following new synonymies are proposed: P. torquatus O. P.- Cambridge, 1908 = P. pulchellus; P. salinarum Denis, 1939 = P. glaucinus; P. glaucinoides Wunderlich, 1987 = P. punctigerus; P. marionschmidti (Schmidt, 1990) = P. pulchellus. Philodromus albopictus Simon, 1875 and P. rubidus Simon, 1870 are considered nomina dubia. Determination of phylogenetic relationships within the group is difficult owing to continuous character variation, resulting in partially incongruent reconstructions using morphological and molecular data (partial mitochondrial cytochrome c oxidase I gene). Dispersal vicariance analysis provides support for a western Mediterranean origin of the group.

scholarly journals Morphological and molecular data reveal a new species of Allium (Amaryllidaceae) from SW Anatolia, Turkey

Phytotaxa ◽  
2015 ◽  
Vol 212 (4) ◽  
pp. 283 ◽  
Author(s):  
İsmail Gökhan Deniz ◽  
İlker Genç ◽  
Duygu Sarı
Keyword(s):  
New Species ◽  
Phylogenetic Tree ◽  
Molecular Data ◽  
Close Relative ◽  
Western Region ◽  
Distribution Map ◽  
Tree Distribution ◽  
Morphological Differences ◽  
Morphological And Molecular Data ◽  
A New Species

Allium undulatitepalum (Amaryllidaceae) is described as a new species from the Antalya Province of Turkey. It belongs to the section Melanocrommyum and is endemic to the south-western region of Turkey. The new species is a close relative of A. orientale, but according to results of the ITS sequences, and based on the morphological differences presented in the description, it is clearly different from its relative. A phylogenetic tree, distribution map, illustrations, pollen and seed microphotographs, karyo-morphology, as well as notes on the biogeography and ecology of the new species are provided.

scholarly journals New molecular sequences for two genera of marine planarians facilitate determination of their position in the phylogenetic tree, with new records for two species (Platyhelminthes, Tricladida, Maricola)

ZooKeys ◽  
2018 ◽  
Vol 781 ◽  
pp. 1-17 ◽  
Author(s):  
Hee-Min Yang ◽  
Ronald Sluys ◽  
Masaharu Kawakatsu ◽  
Gi-Sik Min
Keyword(s):  
Phylogenetic Tree ◽  
New Records ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Molecular Sequences ◽  
Histological Studies ◽  
Anatomical Features ◽  
First Time

For the first time, molecular sequences of the 18S ribosomal DNA were generated for representatives of the genera Obrimoposthia Sluys & Ball, 1989 and Paucumara Sluys, 1989 of the suborder of the marine triclads, or Maricola, by analyzing the species Obrimoposthiawandeli (Hallez, 1906) and Paucumaratrigonocephala (Ijima & Kaburaki, 1916). On the basis of this molecular data the phylogenetic position of these two genera in the phylogenetic tree of the Maricola was determined and compared with their position in the phylogeny based on the analysis of anatomical features. New records for these two species are documented and their taxonomic status is determined on the basis of histological studies.

Species limits in Pteruthius (Aves: Corvida) shrike-babblers: a comparison between the Biological and Phylogenetic Species Concepts

Zootaxa ◽  
2009 ◽  
Vol 2301 (1) ◽  
pp. 29-54 ◽  
Author(s):  
FRANK E. RHEINDT ◽  
JAMES A. EATON
Keyword(s):  
Species Concept ◽  
Molecular Data ◽  
Biological Species ◽  
Species Concepts ◽  
Biological Species Concept ◽  
Phylogenetic Species ◽  
Species Status ◽  
Phylogenetic Species Concept ◽  
Sampling Regime ◽  
Morphological And Molecular Data

The question of how to define a species continues to divide biologists. Meanwhile, the application of different species concepts has led to disparate taxonomic treatments that confound conservationists and other biologists. The most widely followed guidelines to species designation in avian and other vertebrate taxonomy are Ernst Mayr’s Biological Species Concept (BSC) and Joel Cracraft’s version of the Phylogenetic Species Concept (PSC). Although the BSC is considered to be more conservative in its assignment of species status, there is a lack of research demonstrating differences in taxonomic treatment between the BSC and the PSC with reference to a multi-taxon multi-trait study system. We examined the case of five traditionally recognized species of shrike-babbler (Pteruthius) that have recently been divided into 19 species under the PSC. Re-analyzing previous morphological and molecular data and adding new vocal data, we propose a BSC classification of 9 species. However, taking into consideration geographic gaps in the sampling regime, we contend that additional data will likely reduce discrepancies between the total numbers of species designated under the PSC and BSC. The current PSC species total is a likely overestimate owing to species diagnosis based on characters that erroneously appear to be unique to a taxon at low sample size. The current BSC species total as here proposed is a likely underestimate on account of the conservative designation of taxa as subspecies in equivocal cases, e.g. where BSC species status is potentially warranted but may be masked by insufficient data.

A revision of the Trimeresurus puniceus-complex (Serpentes: Viperidae: Crotalinae) based on morphological and molecular data

Zootaxa ◽  
2006 ◽  
Vol 1293 (1) ◽  
pp. 1 ◽  
Author(s):  
PATRICK DAVID ◽  
GERNOT VOGEL ◽  
S. P. VIJAYAKUMAR ◽  
NICOLAS VIDAL
Keyword(s):  
Species Concept ◽  
Distinct Species ◽  
Morphological Characters ◽  
Molecular Data ◽  
Biological Species ◽  
Valid Species ◽  
Biological Species Concept ◽  
Phylogenetic Species Concept ◽  
Morphological And Molecular Data ◽  
A New Species

The brown Asian pitvipers of the genus Trimeresurus related to Trimeresurus puniceus (informal Trimeresurus puniceus-complex) are revised on the basis of morphological and molecular analyses. Variation in morphological characters were investigated among 119 specimens from 62 populations of the whole range of the pitvipers currently known as Trimeresurus puniceus (Boie, 1827), Trimeresurus borneensis (Peters, 1872) and Trimeresurus brongersmai Hoge, 1969. Molecular and morphological analyses clearly differentiate two groups of taxa, referrable to the informal Trimeresurus puniceus-group and Trimeresurus borneensis-group, and confirm the distinct specific status of T. puniceus and T. borneensis. Morphological univariate and multivariate analyses differentiate six clusters of populations that are morphologically diagnosable, of which five are here considered to represent independent lineages and one is placed incertae sedis pending the availability of further specimens. These clusters are considered to be distinct species following the Biological Species Concept and the Phylogenetic Species Concept. One of them is described as a new species, Trimeresurus andalasensis spec. nov. (T. borneensis-group), which includes populations from northern Sumatra. Trimeresurus wiroti Trutnau, 1981 is revalidated to accommodate populations from Thailand and West Malaysia. Trimeresurus borneensis is here considered endemic to Borneo. Trimeresurus puniceus is known from Java and from South Sumatra, but the taxonomy of this species in Sumatra is left unresolved. Also left unresolved is the taxonomic position of specimens from western Sumatra and the Mentawai Archipelago, and from the Natuna Islands and Anamba Islands. Although belonging to the T. puniceus-group, they show some differences to other specimens of the group. They are not referred to any taxon pending the collection of additional specimens. Lastly, Trimeresurus brongersmai is confirmed as a valid species from the Mentawai Archipelago. A key to these taxa is provided.

A new species of Clavariadelphus (Basidiomycota: Clavariadelphaceae) from China based on morphological and molecular data

Phytotaxa ◽  
2020 ◽  
Vol 447 (1) ◽  
pp. 61-67
Author(s):  
LU XIA ◽  
LI FAN
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
North China ◽  
Molecular Data ◽  
Its Sequences ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
Morphological And Molecular Data ◽  
A New Species

Clavariadelphus griseoclavus sp. nov. is described and illustrated from North China. Morphologically, the new species is distinguished from other Clavariadelphus species by its grey to greyish basidiomata. Molecular phylogenetic analysis based on ITS sequences is provided and supports the establishment of the new species.

scholarly journals Molecular characterization of fungi associated with stored soybean (Glycine max L) seeds

2020 ◽  
Vol 36 (2) ◽  
pp. 27-32
Author(s):  
C.G. Ikechi-Nwogu ◽  
F.C. Okene
Keyword(s):  
Fungal Pathogens ◽  
Fungal Species ◽  
Molecular Techniques ◽  
Local Alignment ◽  
Post Harvest ◽  
High Quality Protein ◽  
Search Tool ◽  
Food And Feed ◽  
Glycine Max L

Soybean is an important legume that has high quality protein and oil for food and feed. Despite the importance of this legume, the crop is affected by several post-harvest diseases caused by fungi. A study was carried out to identify the fungal species associated with the seeds of soybean using molecular techniques. The DNA of the isolate, was molecularly characterized using Internal Transcribed Spacer 1 (ITS-1) molecular marker. The isolate DNA sequence, was aligned using the Basic Local Alignment Search Tool for nucleotide (BLASTN) 2.8.0 version of the National Center for Biotechnology Information (NCBI) database. The results showed that the isolate sequence was 98% identical to Diaporthe spp. Voucher VP51, 98% identical to Diaporthe schini isolate L5N71 and 98% identical to Diaporthe schini strain B125. These findings showed that Diaporthe spp. is one of the causal fungal pathogens of post-harvest diseases of soybean seeds. It is anticipated that these results will provide information on culturing Diaporthe species also provide the basis for further study to show their antibiotic and anti-cancerous, enzymes and secondary metabolites producing ability. Keywords: Soybean, Diaporthe schini and RBCL marker

Scytinostroma yunnanense sp. nov. (Russulales, Basidiomycota) evidenced by morphological characteristics and phylogenetic analyses in China

Phytotaxa ◽  
2020 ◽  
Vol 451 (2) ◽  
pp. 145-153
Author(s):  
HUI WANG ◽  
XIAO HE ◽  
CHANG-LIN ZHAO
Keyword(s):  
New Species ◽  
Growth Habit ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Fungal Species ◽  
Its Sequences ◽  
Monophyletic Lineage ◽  
Thin Walled

A new wood-inhabiting fungal species, Scytinostroma yunnanense, is proposed based on morphological and molecular evidences. The species is characterized by an annual growth habit, resupinate basidiomata with cream hymenial surface, a monomitic hyphal system with generative hyphae bearing simple septa, fusiform to cylindrical cystidia and basidiospores (4.5–5.5 × 4.2–5.2 µm) are acyanophilous, subglobose to globose, hyaline, thin-walled, smooth, amyloid. The phylogenetic analyses based on molecular data of ITS sequences showed that the new species formed a monophyletic lineage with a strong support (100% BS, 100% BP, 1.00 BPP) and then was sister to S. duriusculum.

Sign in / Sign up

Export Citation Format

Share Document