scholarly journals Sequence Analysis of the Internal Transcribed Spacer (ITS) Region of the Nuclear Ribosomal DNA (nrDNA), and trnL Intron of Chloroplast DNA (cpDNA) of the Chrysochamela (Fenzl) Boiss. (Brassicaceae) In Turkey

2021 ◽  
Vol 78 (2) ◽  
pp. 147
Author(s):  
Emre SEVİNDİK ◽  
Mehmet Yavuz PAKSOY
Keyword(s):  
Phylogenetic Tree ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Forage Plants ◽  
Brassicaceae Species ◽  
Sequences Analysis ◽  
Industrial Oilseeds ◽  
Large Groups ◽  
Brassicaceae Family

Brassicaceae family is an important one since it includes many economic and significant industrial oilseeds, spices, vegetables and some forage plants. In this study, sequences analysis among Chrysochamela (Brassicaceae) species distributed in Turkey were conducted nrDNA ITS and cpDNA trnL intron sequences. Chrysochamela species were collected and brought to the laboratory. ITS and trnL intron sequences were corrected with BioEdit and FinchTV programs. As a result of the study, ITS nucleotide compound compositions were determined as 22.7% T, 29.1 C, 21.5% A and 26.7% G. The lowest distance was 0.000 and the highest distance was 0.037. The phylogenetic tree obtained using the MEGA 6.0 program consists of two large groups. According to trnL intron sequences 37.9% T, 18.4 C, 28.3% A and 15.5% G. Nucleotide compound compositions were determined. The genetic distance between species was determined between 0.000 and 0.022. Maximum likelihood phylogenetic tree consists of two large groups.  As a result, phylogenetic analyzes using ITS and trnL intron sequences were compatible with each other. It was also in past studies found to be supported by morphological, anatomical and RAPD data.

scholarly journals Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Horticulturae ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 19
Author(s):  
Patricia Coughlan ◽  
James C. Carolan ◽  
Ingrid L. I. Hook ◽  
Lisa Kilmartin ◽  
Trevor R. Hodkinson
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Its Region ◽  
Single Species ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Group Status ◽  
Haplotype Networks

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.

scholarly journals Phylogenetic analysis of the genus Conringia Heist. Ex Fabr. (Brassicaceae) in Turkey based on nuclear (nrITS) and chloroplast (trnL-F) DNA sequences

2021 ◽  
Vol 13 (3) ◽  
pp. 11034
Author(s):  
Emre SEVINDIK ◽  
Melike AYDOGAN ◽  
Mehmet Y. PAKSOY
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nuclear Ribosomal Dna ◽  
Neighbor Joining ◽  
F Region ◽  
Brassicaceae Species ◽  
Nj Tree ◽  
Brassicaceae Family

In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while the trnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic.

Higher-level relationships among the eucalypts are resolved by ITS-sequence data

2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Phylogenetic Groups ◽  
Single Section ◽  
Western Australian ◽  
Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

scholarly journals WildTermitomycesSpecies Collected from Ondo and Ekiti States Are More Related to African Species as Revealed by ITS Region of rDNA

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Victor Olusegun Oyetayo
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Molecular Identification ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Its Sequence ◽  
African Countries ◽  
African Species ◽  
Its Sequence Analysis ◽  
Degree Of Similarity

Molecular identification of eighteenTermitomycesspecies collected from two states, Ondo and Ekiti in Nigeria was carried out using the internal transcribed spacer (ITS) region. The amplicons obtained from rDNA ofTermitomycesspecies were compared with existing sequences in the NCBI GenBank. The results of the ITS sequence analysis discriminated between all theTermitomycesspecies (obtained from Ondo and Ekiti States) andTermitomycessp. sequences obtained from NCBI GenBank. The degree of similarity of T1 to T18 to gene ofTermitomycessp. obtained from NCBI ranges between 82 and 99 percent.Termitomycesspecies from Garbon with ascension number AF321374 was the closest relative of T1 to T18 except T12 that has T. eurhizus and T. striatus as the closet relative. Phylogenetic tree generated with ITS sequences obtained from NCBI GenBank data revealed that T1 to T18 are more related toTermitomycesspecies indigenous to African countries such as Senegal, Congo, and Gabon.

scholarly journals Evaluation of bat adenoviruses suggests co-evolution and host roosting behaviour as drivers for diversity

2021 ◽  
Vol 7 (4) ◽  
Author(s):  
Nkom F. Ntumvi ◽  
Joseph Le Doux Diffo ◽  
Ubald Tamoufe ◽  
Valantine Ngum Ndze ◽  
Jean-Michel Takuo ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Host Species ◽  
Dna Detection ◽  
The Novel ◽  
Recent Past ◽  
Pcr Assays ◽  
Large Groups

Adenoviruses (AdVs) are diverse pathogens of humans and animals, with several dozen bat AdVs already identified. Considering that over 100 human AdVs are known, and the huge diversity of bat species, many bat AdVs likely remain undiscovered. To learn more about AdV prevalence, diversity and evolution, we sampled and tested bats in Cameroon using several PCR assays for viral and host DNA. AdV DNA was detected in 14 % of the 671 sampled animals belonging to 37 different bat species. There was a correlation between species roosting in larger groups and AdV DNA detection. The detected AdV DNA belonged to between 28 and 44 different, mostly previously unknown, mastadenovirus species. The novel isolates are phylogenetically diverse and while some cluster with known viruses, others appear to form divergent new clusters. The phylogenetic tree of novel and previously known bat AdVs does not mirror that of the various host species, but does contain structures consistent with a degree of virus–host co-evolution. Given that closely related isolates were found in different host species, it seems likely that at least some bat AdVs have jumped species barriers, probably in the more recent past; however, the tree is also consistent with such events having taken place throughout bat AdV evolution. AdV diversity was highest in bat species roosting in large groups. The study significantly increased the diversity of AdVs known to be harboured by bats, and suggests that host behaviours, such as roosting size, may be what limits some AdVs to one species rather than an inability of AdVs to infect other related hosts.

scholarly journals Distribution trends of some species of the Brassicaceae family in Latvia

Botanica ◽  
2018 ◽  
Vol 24 (2) ◽  
pp. 124-131
Author(s):  
Ieva Rūrāne ◽  
Pēteris Evarts-Bunders ◽  
Māris Nitcis
Keyword(s):  
Agricultural Land ◽  
Field Studies ◽  
Agricultural Crops ◽  
Bunias Orientalis ◽  
Time Period ◽  
Brassicaceae Species ◽  
Time Periods ◽  
Agricultural Land Management ◽  
Brassicaceae Family ◽  
Distribution Trends

Abstract Rūrāne I., Evarts-Bunders P., Nitcis M., 2018: Distribution trends of some species of the Brassicaceae family in Latvia. - Botanica, 24(2): 124-131. The aim of this paper was to clarify and analyse the distribution trends of some Brassicaceae species (Bunias orientalis, Sisymbrium volgense, Barbarea arcuata, Draba nemorosa and Camelina alyssum) in Latvia. Field studies and the herbarium material analyses were carried out. The distribution trends were analysed by comparing all selected species in three time periods: by 1940, from 1941 to 1990, and from 1991 to the present. The study shows that the distribution of Brassicaceae species such as Bunias orientalis, Sisymbrium volgense, Barbarea arcuata and Draba nemorosa has increased significantly in Latvia during the time period from 1991 to the present, and these species are mostly found on railway, ruderal areas and roadsides, which are important habitats for species distribution. The occurrence of Camelina alyssum has considerably declined or perhaps the species has even disappeared from the flora of Latvia, which has been affected greatly by changes in the cultivation of agricultural crops as well as in agricultural land management.

scholarly journals Ecology, Phylogeny, and Potential Nutritional and Medicinal Value of a Rare White “Maitake” Collected in a Mediterranean Forest

Diversity ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 230 ◽  
Author(s):  
Maria Letizia Gargano ◽  
Georgios I. Zervakis ◽  
Omoanghe S. Isikhuemhen ◽  
Giuseppe Venturella ◽  
Roberta Calvo ◽  
...  
Keyword(s):  
Cold Water ◽  
Water Extract ◽  
Its Region ◽  
Dry Weight ◽  
Field Investigation ◽  
Nutritional Composition ◽  
Nuclear Ribosomal Dna ◽  
Composition Analysis ◽  
Scientific Publications ◽  
Living Tree

Albino Grifola frondosa (Dicks.) Gray “maitake” mushrooms (described as G. albicans Imazeki and then placed in synonymy with G. frondosa) are particularly rare, and the few pertinent records are not treated in scientific publications. A field investigation carried out in Sicily (Italy) led to the collection of an unusual white Grifola specimen at the base of a living tree of Quercus pubescens Willd. s.l. The outcome of sequencing the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) indicated that it belongs to G. frondosa and provided an insight to the phylogenetic relationships within the genus. The results of nutritional composition analysis showed that the albino basidioma possesses relatively high contents of Ca, Fe, K, and Cu and is rather low in Na when compared with literature data on edible mushrooms. Vitamin (B1, B2, B3, B5, B9, and D2) contents ranged from 0.15 to 3.89 mg per 100 g of mushroom dry weight. The cold-water extract of this specimen was effective at inhibiting the growth of Staphylococcus epidermidis ATCC 12228 and Pseudomonas aeruginosa ATCC 15442 at the maximum screening concentration of 50% v/v. In addition, the extract slowed down the ability of Staphylococcus aureus ATCC 43300 to form biofilms. According to data hereby reported, the albino G. frondosa is a culinary-medicinal mushroom with a promising exploitation potential.

PHYLOGENY AND SPECIES RELATIONSHIPS IN JASIONE (CAMPANULACEAE) WITH EMPHASIS ON THE ‘MONTANA-COMPLEX’

2005 ◽  
Vol 62 (1-2) ◽  
pp. 29-51 ◽  
Author(s):  
S. PÉREZ-ESPONA ◽  
F. SALES ◽  
I. HEDGE ◽  
M. MÖLLER
Keyword(s):  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Shetland Islands ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Recent Origin ◽  
Higher Rank ◽  
Sample Set ◽  
Larger Sample

The evolutionary relationships of several, mainly Iberian, Jasione taxa (Campanulaceae) were investigated using molecular data. A parsimony analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA was partially successful in elucidating some interspecific alliances. One of the main clades included three morphologically rather disparate species from S Spain and Morocco which might indicate that these areas were refugia during the last glaciations. The fact that most of the other taxa fell in a large polytomy suggests a recent origin of these species. Amplified fragment length polymorphisms (AFLPs) were analysed for a larger sample set of two taxa from within the ITS polytomy to assess the partition of genetic variation between and within populations. All the British accessions named J. montana var. montana were found to be close to those so-named from Spain. However, individual accessions of J. montana var. montana from Argyll (Scotland), Devon (SW England) and the Shetland Islands proved to be genetically different from each other. This might suggest a low level of genetic diversification from a common progenitor due to a rapid northward migration. It is proposed that J. montana var. bracteosa and J. maritima var. sabularia merit recognition at higher rank. The possibility that J. montana vars gracilis and latifolia are mere repetitive segregants of J. montana var. montana is considered.

DNA sequencing and genetic diversity of the 18S–26S nuclear ribosomal internal transcribed spacers (ITS) in nine Antarctic moss species

2005 ◽  
Vol 17 (3) ◽  
pp. 377-384 ◽  
Author(s):  
M.L. SKOTNICKI ◽  
A.M. MACKENZIE ◽  
M.A. CLEMENTS ◽  
P.M. SELKIRK
Keyword(s):  
Dna Sequencing ◽  
Simple Technique ◽  
Ross Sea ◽  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Taxonomic Identification ◽  
Moss Species ◽  
Antarctic Moss

We have sequenced the 18S–26S nuclear ribosomal DNA ITS region from the genome of nine different moss species from the Ross Sea region of Antarctica. This relatively quick and simple technique enables these species to be readily distinguished, facilitating their taxonomic identification. Only a single moss shoot is required, and for identification of these bryophytes it is only necessary to determine a few hundred nucleotides of the DNA sequence in a single sequencing reaction. Several previously unidentified Antarctic moss specimens were readily characterized by comparison with ITS sequences of known moss species. The relationships between species and locations previously detected by the RAPD (Random Amplified Polymorphic DNA) technique were confirmed by DNA sequencing, demonstrating that the two techniques can be complementary for molecular analysis of the ecology of mosses in Antarctica.

Sign in / Sign up

Export Citation Format

Share Document