scholarly journals Characterization of rbcL and trnL Plastid DNA Sequences of Vuralia turcica (Fabaceae; Papilionoideae)

2019 ◽  
Vol 7 (6) ◽  
pp. 908
Author(s):  
Dilek Tekdal
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Tree ◽  
Plant Species ◽  
Dna Sequences ◽  
Its Region ◽  
Plastid Dna ◽  
Accession Number ◽  
Molecular Information

Vuralia turcica is endemic to Turkey and currently endangered. Little molecular information is available for this plant. Previous characterization and classification of V. turcica have been based on the DNA sequences of the ITS region. Molecular markers are essential for studying of genotyping and biogeography, but any of each marker is not enough to characterize a plant species in its use alone. In this study, the chloroplast rbcL and trnL regions were amplified in V. turcica using the primers that have been published in the previous studies. Successfully amplified DNA fragments were extracted and commercially sequenced. The partial rbcL and trnL sequences were submitted to the NCBI database (accession number KX164510, KX164511, respectively). Amplified both DNA of two regions of rbcL and trnL were used to construct a phylogenetic tree.

Towards a monophyletic classification of Lejeuneaceae III: the systematic position of Leiolejeunea

Phytotaxa ◽  
2014 ◽  
Vol 170 (3) ◽  
pp. 187 ◽  
Author(s):  
ALFONS SCHÄFER-VERWIMP ◽  
KATHRIN FELDBERG ◽  
SHANSHAN DONG ◽  
HUUB VAN MELICK ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Its Region ◽  
Systematic Position ◽  
Leaf Cell ◽  
Oil Bodies ◽  
Sister Relationship ◽  
First Time

The derived liverwort Leiolejeunea grandiflora was recollected at the type locality in Jamaica after more than 100 years. The characteristics of its oil bodies were described for the first time based on the new collections. Each leaf cell possesses 2-4(-6) rather small, subhomogeneous to very finely segmented, subglobose to ellipsoidal, colorless oil bodies. The plants were either dioicous or autoicous. DNA sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region were obtained for two accessions of Leiolejeunea to enable the inference of the phylogenetic relationships of these plants. Based on Bayesian inference of phylogeny as well as maximum parsimony and maximum likelihood analyses of a dataset including 87 representatives of Lejeuneaceae, Leiolejeunea was found as the putative sister to either Echinolejeuneinae or Cheilolejeuneinae. Thus, we propose the new monogeneric subtribe Leiolejeuneinae with relationships to Cheilolejeuneinae and Echinolejeuneinae. The analyses included also one accession of the generitype of Cheilolejeunea, C. decidua [= Cheilolejeunea adnata]. This species was found in a well supported sister relationship with Cystolejeunea. To avoid nomenclatural confusion, we propose a wide genus concept for Cheilolejeunea including Aureolejeunea, Cyrtolejeunea, Cystolejeunea, Evansiolejeunea, Leucolejeunea, and Omphalanthus.

scholarly journals Survey, Identification, and Characterization of Cylindrocarpon-Like Asexual Morphs in Spanish Forest Nurseries

Plant Disease ◽  
2018 ◽  
Vol 102 (11) ◽  
pp. 2083-2100 ◽  
Author(s):  
Beatriz Mora-Sala ◽  
Ana Cabral ◽  
Maela León ◽  
Carlos Agustí-Brisach ◽  
Josep Armengol ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Elongation Factor ◽  
Its Region ◽  
Phylogenetic Position ◽  
Translation Elongation ◽  
Forest Nurseries ◽  
Asexual Morphs ◽  
Identification And Characterization ◽  
Elongation Factor 1

Cylindrocarpon-like asexual morphs infect herbaceous and woody plants, mainly in agricultural scenarios, but also in forestry systems. The aim of the present study was to characterize a collection of Cylindrocarpon-like isolates recovered from the roots of a broad range of forest hosts from nurseries showing decline by morphological and molecular studies. Between 2009 and 2012, 17 forest nurseries in Spain were surveyed and a total of 103 Cylindrocarpon-like isolates were obtained. Isolates were identified based on DNA sequences of the partial gene regions histone H3 (his3). For the new species, the internal transcribed spacer and intervening 5.8S nrRNA gene (ITS) region, β-tubulin (tub2), and translation elongation factor 1-α (tef1) were also used to determine their phylogenetic position. Twelve species belonging to the genera Cylindrodendrum, Dactylonectria, and Ilyonectria were identified from damaged roots of 15 different host genera. The species C. alicantinum, D. macrodidyma, D. novozelandica, D. pauciseptata, D. pinicola, D. torresensis, I. capensis, I. cyclaminicola, I. liriodendri, I. pseudodestructans, I. robusta, and I. rufa were identified. In addition, two Dactylonectria species (D. hispanica sp. nov. and D. valentina sp. nov.), one Ilyonectria species (I. ilicicola sp. nov.), and one Neonectria species (N. quercicola sp. nov.) are newly described. The present study demonstrates the prevalence of this fungal group associated with seedlings of diverse hosts showing decline symptoms in forest nurseries in Spain.

Molecular markers indicate intraspecific variation in the control ofEchinochloaspp. with quinclorac

Weed Science ◽  
1999 ◽  
Vol 47 (3) ◽  
pp. 310-315 ◽  
Author(s):  
Nuria Lopez-Martinez ◽  
Antonio Pujadas Salva ◽  
Robert P. Finch ◽  
George Marshall ◽  
Rafael De Prado
Keyword(s):  
Molecular Markers ◽  
Molecular Characterization ◽  
Intraspecific Variation ◽  
Morphological Diversity ◽  
Differential Sensitivity ◽  
Yield Losses ◽  
Natural Tolerance ◽  
Botanical Classification

Some species of the genusEchinochloaare troublesome weeds in rice fields. The taxonomy of this genus leads to confusion in many cases due to its great morphological diversity. Because of the differential sensitivity to the herbicide quinclorac shown byEchinochloaspp., it was necessary to assess the botanical and molecular characterization of this weed.Echinochloa colonum, E. oryzoides, andE. oryzicolawere very susceptible to quinclorac treatment; by contrast,E. crus-galliandE. hispidulashowed some degree of natural tolerance. Physiological and molecular results agreed with the botanical classification of the genusEchinochloain Flora Europea. The importance of these results is due to yield losses produced by the infestation ofEchinochloaand the need for a strategy forEchinochloamanagement depending on the distribution of theEchinochloaspecies.

scholarly journals Prevalence and Molecular Characterization of Cysticercus tenuicollis Isolated from Some Intermediate Host in Kurdistan-Iraq

2018 ◽  
pp. 177-182
Author(s):  
Abdullah Ahmed Hama ◽  
Rostam Hama Zorab ◽  
Fatima Mohammed Ali ◽  
Awaz M. Salih ◽  
Amer Abdullah Hassan
Keyword(s):  
Hydatid Cyst ◽  
Molecular Characterization ◽  
Dna Sequences ◽  
Prevalence Rate ◽  
Accession Number ◽  
Taenia Hydatigena ◽  
Sheep And Goats ◽  
Cysticercus Tenuicollis ◽  
Nucleotide Sequence Alignment

Cysticercus tenuicollis (C. tenuicollis) is the larval stage infection of Taenia hydatigena, a common tapeworm of dogs and other Canidae, which has a wide range of intermediate hosts including sheep, goat, cattle, deer, camel, horse, human and other wild ruminants, the disease spreads through a contaminated water, soil and food with feces of infected dogs or other carnivores, T. hydatigena lives in the intestinal of the definitive host (carnivores) and excretes a huge number of eggs with feces daily. The present study conducted to determine the prevalence rate and molecular characterization of C. tenuicollis among sheep and goats in Sulaimani province. A total of 14088 slaughtered animals were inspected postmortem from the new Sulaimani abattoir comprise, which involves 13395 sheep and 693 goats. The selected cysts were preserved in 70% Ethanol for DNA extraction and molecular study,  The mt-CO1 gene was amplified with a conventional polymerase chain reaction (PCR), the PCR product purified and DNA sequencing for reverse and forward strands was determined by a genetic analyzer, the obtained sequences aligned with the DNA sequences of T. hydatigena in Iran, Turkey and Palestine, which deposited in GenBank under the following accession number (JQ710588), (JN827307) and ( KM032284) respectively. The prevalence rate of C. tenuicollis was 2.63% in sheep and 2.58% in goats. This result shows no significant differences of C. tenuicollis between sheep and goats (p>0.05). The nucleotide sequence alignment of cytochrome oxidase subunit 1 (CO 1) gene revealed that the amplified DNA fragment is belong to Taenia hydatigena and Echinococcus granulosus and the nucleotide sequences of T. hydatigena deposited in GenBank under accession number (MH638348). This finding concludes that the amplification of mt-CO1 gene cannot be depended on discriminate hydatid cyst and C. tenuicollis while the partial DNA sequences of mt-CO1 gene are significantly valuable to differentiate C. tenuicollis from hydatid cyst, which is completely different in the pathology and control.

Polyphyly of the iconic cactus genus Turbinicarpus (Cactaceae) and its generic circumscription

2019 ◽  
Vol 190 (4) ◽  
pp. 405-420 ◽  
Author(s):  
Monserrat Vázquez-sánchez ◽  
Daniel Sánchez ◽  
Teresa Terrazas ◽  
Alejandro De La Rosa-Tilapa ◽  
Salvador Arias
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Chihuahuan Desert ◽  
Plastid Dna ◽  
Morphological Characters ◽  
Species Relationships ◽  
Biogeographic History ◽  
Main Region

AbstractGeneric circumscription and species relationships in several lineages in Cactaceae tribe Cacteae remain unresolved. Turbinicarpus s.l. is one of the most species-rich genera in Cacteae, with its centre of distribution in the Chihuahuan Desert, Mexico. We reconstructed a phylogenetic tree of Turbinicarpus s.l. with Bayesian inference, using plastid DNA sequences and morphological characters, and inferred biogeographic history in order to understand their relationships. Our results supported the recognition of three different monophyletic lineages: Kadenicarpus, Rapicactus and Turbinicarpus. Kadenicarpus is endemic to the southernmost part of the Chihuahuan Desert in the states of Hidalgo and Querétaro. Rapicactus and Turbinicarpus are distributed in the main region of the Chihuahuan Desert where they have areas of overlap.

Molecular characterization of European Pygorchis Looss, 1899

2021 ◽  
Vol 95 ◽  
Author(s):  
P. Heneberg ◽  
J. Sitko
Keyword(s):  
Molecular Characterization ◽  
Dna Sequences ◽  
Type Species ◽  
Molecular Phylogenetics ◽  
Morphological Description ◽  
Central Asian ◽  
First Time

Abstract Adult trematodes of the genus Pygorchis Looss, 1899 (Trematoda: Philophthalmidae) parasitize the cloaca of birds. The genus contains three species, all of which are rarely reported and molecular phylogenetics of which have not been applied. The absence of reference DNA sequences limit studies of their indistinct larval forms. Based on the materials that were obtained from birds of the Czech origin, we performed a molecular characterization of both currently known Pygorchis spp., which are known from the Palearctic, the type species Pygorchis affixus Looss, 1899 and Pygorchis alakolensis Zhatkanbaeva, 1967, and provided morphological description of the examined P. alakolensis specimen. We found that the two species were of similar dimensions; the only difference was in the position of testes and in the extent of vitelline follicles. However, the position of testes in P. affixus was variable, and approximately 10% of examined P. affixus individuals had testes positioned obliquely. The second feature that allows differential diagnostic, the extent of vitelline follicles, was more reproducible as the vitelline follicles of P. affixus did not extend beyond the intestinal caeca, or, in exceptional cases, they extended them at only one side. In the examined P. alakolensis individual, the testes were positioned obliquely, and the vitelline follicles extended beyond the intestinal caeca. We reported P. alakolensis for the first time from Europe; previously, it was known only from Central Asian lakes and rivers. We confirmed the classification of Pygorchis into Philophtalmidae.

Phylogenetic relationships in Pterostylidinae (Cranichideae: Orchidaceae): combined evidence from nuclear ribomsomal and plastid DNA sequences

2011 ◽  
Vol 59 (2) ◽  
pp. 99 ◽  
Author(s):  
Mark A. Clements ◽  
J. Tupac Otero ◽  
Joseph T. Miller
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Its Region ◽  
Plastid Dna ◽  
Classification Systems ◽  
Parsimony Analysis ◽  
Internal Support ◽  
Clade B ◽  
Clade C

A study to evaluate the relationships in subtribe Pterostylidinae (Cranichideae: Orchidaceae) was undertaken using DNA sequences from the nuclear ribosomal ITS region (256 taxa) and plastid matK (subset of 37 taxa). Parsimony analysis of nuclear, plastid and combined datasets revealed that there is strong support for the monophyly of Pterostylidinae, and three major groups therein. Clades A–C contain nine, possibly 10, identifiable groups supported by morphological synapomorphies. Clade A comprises the following two major, strongly supported groups that correlate with morphological synapomorphies: (1) Speculantha (including Petrorchis) and (2) Linguella and Eremorchis, sister to an unresolved polytomy containing Taurantha, a paraphyletic Crangonorchis and polyphyletic Diplodium. There is no support for continued recognition of Taurantha, Crangonorchis, Linguella and Eremorchis, all of which are embedded within the broader, strongly supported, monophyletic Diplodium. Clade B represents true Pterostylis. Clade C contains the morphologically disparate Bunochilus, Hymenochilus, Oligochaetochilus, Pharochilum, Plumatichilos, Stamnorchis and Urochilus (including Ranorchis) in a partially resolved tree. There is strong molecular and morphological synapomorphic internal support for the recognition of these taxa as genera. Our results revealed that none of the presently proposed classification systems for Pterostylidinae truly accounts for the underlying phylogenetic signal. A streamlined classification system, therefore, seems warranted, although further research based on a larger plastid DNA dataset is required to elucidate relationships in Clade C.

scholarly journals A review on the molecular characterization of digenean parasites using molecular markers with special reference to ITS region

2015 ◽  
Vol 52 (3) ◽  
pp. 167-187 ◽  
Author(s):  
K. Choudhary ◽  
A. Kumar Verma ◽  
S. Swaroop ◽  
N. Agrawal
Keyword(s):  
Molecular Markers ◽  
Its Region ◽  
Farm Animals ◽  
New Genera ◽  
Specific Level ◽  
Rdna Sequences ◽  
Region Data ◽  
Identification Of Species ◽  
Immense Potential

Abstract The rDNA region of eukaryotes has the immense potential to resolve the evolutionary and phylogeny problems using molecular markers. As evident from the present review, ITS region data is considered for interpretation of inter and intra-specific variations of 136 studies of 33 families including 78 genus and 114 species affecting individuals worldwide. Along with ITS-1 and ITS-2 region in 29 studies 18S region, in 38 studies 28S region and in 43 studies mitochondrial genes (COI and NDI) were also analyzed. Three new genera (Allobilharzia gen. nov., Caulanus gen. nov., and Latuterus gen. nov.) and 49 new species were discovered. Only 47 studies expressed variations at intra-specific and inter-specific level in complete ITS region, ITS-1 and ITS-2 rDNA sequences due to differences in nucleotide positions. According to the findings ITS region is more reliable and precise marker for demarcation and identification of species in combination of other DNA markers. Major studies were involved around the parasites of families Fasciolidae, Schistosomatidae, Opisthorchidae, Paragonimidae and Paramphistomidae, Clinostomidae, Diplostomidae, Haploporidae, among others infecting humans, farm animals, birds, fishes, reptiles and amphibians on the clinical basis. In future, molecular and bioinformatics aspects based on genetic variations will lead to explore the untouched areas of trematodes.

scholarly journals Molecular characterization of stinkhorn fungus Aseroë coccinea Imazeki et Yoshimi ex Kasuya 2007 (Basidiomycota: Agaricomycetes: Phallales) from India

2020 ◽  
Vol 12 (4) ◽  
pp. 15530-15534
Author(s):  
Vivek Bobade ◽  
Neelesh Dahanukar
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Tree ◽  
Molecular Characterization ◽  
Western Ghats ◽  
Fungal Diversity ◽  
Morphological Characters ◽  
First Report ◽  
Western Ghats Of India ◽  
Generic Position

In this note we provide the first report of stinkhorn fungus Aseroë coccinea from northern Western Ghats of India and first report of this species from outside its type locality in Japan. In addition to the morphological characters, we also provide sequences for two molecular markers and provide a phylogenetic tree, which questions the generic position of the species. Our report highlights the need for more exploratory surveys for understanding diversity, distribution and taxonomy of Phallales and in general fungal diversity of India.

scholarly journals Identification and Characterization of Colletotrichum Species Associated with Anthracnose Disease of Camellia oleifera in China

Plant Disease ◽  
2020 ◽  
Vol 104 (2) ◽  
pp. 474-482 ◽  
Author(s):  
Yixun Wang ◽  
Jing-Yuan Chen ◽  
Xiaowen Xu ◽  
Junyong Cheng ◽  
Lu Zheng ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Economic Losses ◽  
Camellia Oleifera ◽  
Colletotrichum Species ◽  
Recent Developments ◽  
Serious Disease

Tea-oil tree (Camellia oleifera Abel) is an important edible oil woody plant with a planting area over 3,800,000 hectares in southern China. Anthracnose is a serious disease of tea-oil tree in southern China, causing severe economic losses and posing a huge threat to the Ca. oleifera industry. Based on recent developments in the classification of Colletotrichum species, the objective of this study was to identify Colletotrichum species associated with tea-oil tree and examine their pathogenicity on leaves and fruits of Ca. oleifera. In total, 232 isolates were obtained from Ca. oleifera leaves and fruits with anthracnose symptoms. These isolates were further characterized based on morphology and multilocus phylogenetic analyses using partial DNA sequences at the ribosomal internal transcribed spacer regions and β-tubulin, actin, calmodulin, glyceraldehyde-3-phosphate dehydrogenase, and chitin synthase-encoding genes. The fungal isolates belong to five species: C. camelliae, C. fructicola, C. siamense, C. aenigma, and C. gloeosporioides. C. camelliae was the most predominant and widely distributed species on fruits of Ca. oleifera (91.4%), followed by C. fructicola (6.3%). However, C. fructicola was common and widely distributed species on leaves (75.9%), followed by C. camelliae (17.2%). There was no evidence of geographical specialization of the different species. Pathogenicity assays showed that all tested isolates, including 20 of C. camelliae, 11 of C. fructicola, four of C. siamense, two of C. aenigma, and one of C. gloeosporioides, were pathogenic to leaves and fruits of Ca. oleifera. Among the five species, C. camelliae species showed strong pathogenicity on both leaves and fruits of Ca. oleifera, and C. fructicola, C. siamense, C. aenigma, and C. gloeosporioides all showed weak pathogenicity on both leaves and fruits. No relationship was found between origin of isolates and their virulence. This is the first description of C. camelliae, C. fructicola, C. siamense, and C. gloeosporioides from the fruits of Ca. oleifera in China.

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