Genetic diversity of Amsonia orientalis

Biologia ◽  
2014 ◽  
Vol 69 (6) ◽  
Author(s):  
Cem Gürkanli ◽  
İbrahim Özkoç ◽  
Emine Aydin ◽  
Arda Acemi ◽  
Fazıl Özen
Keyword(s):  
Genetic Diversity ◽  
Plant Species ◽  
Intergenic Spacer ◽  
Its Region ◽  
Close Relation ◽  
Morphological Characters ◽  
Molecular Data ◽  
Systematic Position ◽  
Rdna Its ◽  
Threatened Plant Species

AbstractAmsonia orientalis Decne. (Apocynaceae), is a rare and threatened plant species which is located only in a constricted area in northeast of Greece and northwest of Turkey in the world. Although phylogenetic analysis depending on nucleotide sequences of genes from different sources (nucleus, mitochondria and chloroplast) became a major tool for classification of plant species, there is still a big lack of information about A. orientalis in the international molecular data bases such as NCBI. In the current study, we phylogenetically analyzed three commonly used molecular markers (18S rDNA, 18S-28S rDNA-ITS region and trnL-F intergenic spacer) from A. orientalis samples collected from Turkey to determine the genetic diversity and also to question the systematic position of A. orientalis. As a result, A. orientalis samples clearly showed close relation with Alyxieae tribe rather than Vinceae. And this result brings the necessity to reconsider the morphological characters that have used to delimit the tribes of Rauvolfioideae.

scholarly journals Amanita subjunquillea and its ectomycorrhizal association, reported as new for Pakistan

Mycotaxon ◽  
2019 ◽  
Vol 134 (3) ◽  
pp. 413-423
Author(s):  
Muhammad Ishaq ◽  
Arooj Naseer ◽  
Munazza Kiran ◽  
Muhammad Fiaz ◽  
Abdul Nasir Khalid
Keyword(s):  
Its Region ◽  
Morphological Characters ◽  
Molecular Data ◽  
Sequence Analyses ◽  
Dark Orange ◽  
Ectomycorrhizal Roots ◽  
Morphological And Molecular Data ◽  
Quercus Floribunda ◽  
First Time ◽  
Ectomycorrhizal Association

Amanita subjunquillea and its ectomycorrhizal association are reported for the first time from moist temperate Himalayan forests of Pakistan. The sample was studied based on morphological characters and nucleotide sequence analyses of the ITS region generated from basidiomata and ectomycorrhizal roots of Quercus floribunda. Our collection differs from the type in its dark orange pileus disc and pale yellow margins. Remaining morphological and molecular data are consistent with previously reported specimens. This represents the first report of A. subjunquillea from Pakistan.

scholarly journals Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region

Horticulturae ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 87
Author(s):  
Kumpei Shiragaki ◽  
Shuji Yokoi ◽  
Takahiro Tezuka
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Wild Species ◽  
Morphological Characteristics ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Rdna Its ◽  
Rdna Its Region ◽  
Genus Capsicum

The genus Capsicum is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in Capsicum. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 Capsicum accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in Capsicum accessions. Specific morphological characteristics were found in C. annuum, C. baccatum, and C.pubescens. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding C. annuum, suggesting that incomplete concerted evolution occurred in rDNA-ITS of Capsicum. The genetic diversity was evaluated using nucleotide polymorphism and diversity. C. annuum had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for C. annuum, C. baccatum, and C. pubescens. The C. chinense clade existed in the C. frutescens clade, implying that it was a cultivated variant of C. frutescens. C. chacoense likely belonged to the C. baccatum complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated Capsicum species.

scholarly journals Molecular Detection of Bartonella Sp. in Wild Ruminants and Analysis of its Genetic Diversity on the Basis of 16S–23S Rrna Intergenic Spacer (ITS)

2012 ◽  
Vol 56 (1) ◽  
pp. 15-19
Author(s):  
Małgorzata Adamska
Keyword(s):  
Genetic Diversity ◽  
Cervus Elaphus ◽  
Phylogenetic Trees ◽  
Red Deer ◽  
Roe Deer ◽  
Intergenic Spacer ◽  
Capreolus Capreolus ◽  
Its Region ◽  
Its Sequences ◽  
23S Rrna

Abstract The aim of this study was to describe the state of infection of roe deer (Capreolus capreolus) and red deer (Cervus elaphus) by Bartonella sp. in North-Western Poland through PCR detection of Bartonella 16S-23S rRNA ITS region in isolates of animal tissues, and also to describe the genetic diversity of detected Bartonella species based on molecular analysis of ITS. The multiple alignment analysis of ITS sequences was carried out, and homology matrices and phylogenetic trees were constructed. The DNA of Bartonella sp. was detected in tissues of 45.6% (36/79) C. capreolus and of 50% (15/30) C. elaphus. Products of two different sizes were detected: 317 bp, characteristic for B. schoenbuchensis, and 198 bp, characteristic for B. bovis. The obtained results suggest that roe and red deer are potential reservoirs of Bartonella sp. Most of the analysed ITS sequences was not specific for one host species. In constructed phylogenetic trees, sequences obtained from roe and red deer clustered together. These results suggest a lack of host specificity of most detected B. schoenbuchensis and B. bovis intraspecies strains

Cytogenetic and sequence comparison of adultPhyllodistomum(Digenea: Gorgoderidae) from the three-spined stickleback with larvae from two bivalves

Parasitology ◽  
2004 ◽  
Vol 129 (6) ◽  
pp. 771-778 ◽  
Author(s):  
R. PETKEVIČIŪTĖ ◽  
V. STUNŽĖNAS ◽  
G. STANEVIČIŪTĖ
Keyword(s):  
Developmental Stages ◽  
Its Region ◽  
Morphological Characters ◽  
Molecular Data ◽  
Chromosome Morphology ◽  
Published Data ◽  
Larval Stages ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
High Level

Due to the low informative value of available morphological characters, cytogenetic and molecular methods, based on rDNA sequencing, were used to characterize adult and larval stages ofPhyllodistomumspp. Species studied have 18 chromosomes with comparable absolute and relative lengths. Conventional Giemsa staining and karyometric analysis revealed clear differences in chromosome morphology of larvalPhyllodistomumspp. infecting two bivalve host species,Sphaerium corneumandPisidium amnicum. However, karyotypes of adultP. foliumfrom three-spined sticklebacks and larval stages fromS. corneumappear almost identical both with respect to the relative lengths and centromeric indices of the corresponding chromosome pairs. The entire internal transcribed spacer (ITS) region (ITS-1, 5.8S and ITS-2) and the D1-D3 region of 28S gene were sequenced and compared. Again, sufficient differences were observed between larvalPhyllodistomumspp., while adultP. foliumand larvae fromS. corneumshowed a high level of similarity. So, both cytogenetic and molecular data support the suggestion that they represent developmental stages of the same species. The results were compared with published data obtained by cytogenetic and molecular studies on the otherPhyllodistomumspecies. Differences revealed in karyotype and rDNA sequences leads to the conclusion that the cercariaeum ofP. foliumsensu Sinitsin, 1905 could not be regarded as the larva of adultP. foliumfrom three-spined stickleback.

scholarly journals Genetic diversity in threatened plant species Alnus nitida (Spach.) Endel

2020 ◽  
Vol 7 (3) ◽  
pp. 314-318
Author(s):  
Muhammad Khalil Ullah Khan ◽  
Noor Muhammad ◽  
Nisar Uddin ◽  
Niaz Ali ◽  
Muhammad Umer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Species ◽  
Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Plant Conservation ◽  
Protein Characterization ◽  
Threatened Plant ◽  
Threatened Plant Species ◽  
Sds Page ◽  
Species Specific

Alnus nitida (Spach) Endl. is an ethnobotanically important threatened plant species. The genetic diversity among the 50 different genotypes of Alnus nitida was carried out using sodium dodecyl sulfate poly acrylamide gel electrophoresis (SDS-PAGE) characterization. A considerable amount of genetic diversity (90%) was observed among the genotypes of A. nitida. The protein characterization was carried out on 12% gel electrophoresis. A total of 10 protein bands were detected in A. nitida genotypes. SDS-PAGE procedure is a useful method for the investigation of both genetic diversity and phylogenetic relationship. Especially, B-5 was monomorphic in A. nitida genotypes and was considered as species specific. All other bands/loci were polymorphic. These polymorphic bands displayed 12, 16, 72, 88, 2, 44, 84, 54 and 12 percent variation respectively. In the present examination, the high intra-specific diversity was observed representing SDS-PAGE is a powerful tool for determining the genetically diverse germplasms in A. nitida. The results obtained by this study could be helpful in the identification and selection of desired genotypes of Alnus nitida for conservation programmes in future. Today, there is still a need to assess genetic variation and protect genetic resources, especially of wild species for prospective benefits in plant conservation programmes.

scholarly journals How to resolve cryptic species of polypores: an example in Fomes

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Ursula Peintner ◽  
Regina Kuhnert-Finkernagel ◽  
Viana Wille ◽  
Franco Biasioli ◽  
Anton Shiryaev ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Growth Rates ◽  
Species Delimitation ◽  
Its Region ◽  
Morphological Characters ◽  
Rdna Its ◽  
Pure Cultures ◽  
Rdna Its Region ◽  
The Mediterranean ◽  
Physiological Characters

Abstract Species that cannot be easily distinguished based on morphology, but which form distinct phylogenetic lineages based on molecular markers, are often referred to as cryptic species. They have been proposed in a number of fungal genera, including the basidiomycete genus Fomes. The main aim of this work was to test new methods for species delimitation in cryptic lineages of polypores, and to define useful characters for species identification. A detailed examination of a number of different Fomes strains that had been collected and isolated from different habitats in Italy and Austria confirmed the presence of distinct lineages in the Fomes fomentarius clade. Our zero hypothesis was that the Mediterranean strains growing on Quercus represent a species which can be delimited based on morphological and physiological characters when they are evaluated in statistically relevant numbers. This hypothesis was tested based on phylogenetic analysis of the rDNA ITS region, morphological characters of basidiomes and pure cultures, growth rates and optimum growth temperature experiments, mycelial confrontation tests, enzyme activity tests and volatile organic compound (VOC) production. The Mediterranean lineage can unambiguously be delimited from F. fomentarius. A syntype of an obscure and previously synonymized name, Polyporus inzengae, represents the Mediterranean lineage that we recognize as Fomes inzengae, a distinct species. The rDNA ITS region is useful for delimitation of Fomes species. Moreover, also a variety of morphological characters including hymenophore pore size, basidiospore size, and diameter of skeletal hyphae are useful delimiting characters. The ecology is also very important, because the plant host appears to be a central factor driving speciation. Physiological characters turned also out to be species-specific, e.g. daily mycelial growth rates or the temperature range of pure cultures. The production of VOCs can be considered as a very promising tool for fast and reliable species delimitation in the future.

The genealogy of geebungs: phylogenetic analysis of Persoonia (Proteaceae) and related genera in subfamily Persoonioideae

2018 ◽  
Vol 31 (2) ◽  
pp. 166
Author(s):  
Gareth D. Holmes ◽  
Peter H. Weston ◽  
Daniel J. Murphy ◽  
Carolyn Connelly ◽  
David J. Cantrill
Keyword(s):  
Western Australia ◽  
New Caledonia ◽  
Plastid Dna ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Rdna Its ◽  
Eastern Australia ◽  
Group Relationships ◽  
Informal Groups

Proteaceae subfamily Persoonioideae, as presently circumscribed, consists of the monogeneric tribe Placospermeae (Placospermum) and the tribe Persoonieae. The latter comprises the diverse genus Persoonia and monospecific genera found in New Zealand (Toronia), New Caledonia (Garnieria) and south-western Western Australia (Acidonia). Persoonia has 101 species distributed across Australia and has been classified into 11 informal groups. Using data derived from plastid DNA (trnL–trnF region), nuclear rDNA (ITS) and morphological characters, we constructed a phylogeny of Persoonioideae and compared the results to the existing classification. Bayesian and parsimony analyses indicated that Persoonia, as currently defined, is non-monophyletic. The molecular data and combined molecular and morphological data place Toronia in a moderately well supported clade with the monophyletic Rufiflora group of Persoonia from Western Australia. This clade is sister to Acidonia, Garnieria and the remaining Persoonia species. Of the other informal groups in Persoonia, the Teretifolia, Quinquenervis, Laurina, Arborea, Graminea and Chapmaniana groups are supported as monophyletic. The Lanceolata group can be re-circumscribed to be monophyletic by the addition of P. elliptica R.Br. (Longifolia group) and the Dillwynioides group. Relationships within this large, geographically widespread clade are largely unresolved and low DNA-sequence variation within it suggests a recent radiation followed by isolation in south-western and eastern Australia. All endemic Tasmanian Persoonia (Gunnii group taxa) are unresolved at the second-most basal node of the Persoonieae. Our results suggest that the Rufiflora group should be treated as a new genus and that the infrageneric taxonomy of Persoonia requires minor amendment.

Pseudosperma albobrunneum sp. nov. from coniferous forests of Pakistan

Mycotaxon ◽  
2021 ◽  
Vol 136 (2) ◽  
pp. 361-372
Author(s):  
Sana Jabeen ◽  
Zainab ◽  
Hira Bashir ◽  
Abdul Nasir Khalid
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Its Region ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Coniferous Forests ◽  
Molecular Phylogenetic ◽  
Khyber Pakhtunkhwa Province ◽  
A New Species

A new species, Pseudosperma albobrunneum, is described and illustrated. The specimens are from different areas of Khyber Pakhtunkhwa province, Pakistan. The identification is based on morphological characters, in combination with molecular phylogenetic analysis of sequences of the ITS region of nuclear ribosomal DNA. The species is found distinct morphologically from all closely related taxa, and molecular data confirm its novelty.

Genetic diversity of the relict moss Rhytidium rugosum (Hypnales) in Europe inferred from the ITS region (nrDNA)

Biologia ◽  
2011 ◽  
Vol 66 (1) ◽  
Author(s):  
Marko Sabovljević ◽  
Jan-Peter Frahm
Keyword(s):  
Genetic Diversity ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Data Sampling ◽  
Migration Routes ◽  
High Genetic Diversity ◽  
Moss Species ◽  
Asian Populations ◽  
Survival Potential

AbstractPost-glacial survival, potential migration routes, genetic diversity and phylogeography of the boreal moss species Rhytidium rugosum have been studied. This species is considered to be one of glacial relics of the wide but scattered Holarctic range. According to molecular data sampling from the selected European, American and Asian populations high genetic diversity of this species is present, even if this species is mostly sterile and produced sex organs extremely rarely and spread mostly asexually. Analysing the internal transcribed spacer (ITS) of the nuclear ribosomal DNA, it can be concluded that the populations of this species survived glaciations in various places in Europe and settled and re-settled present range space in various times from various refuges.

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