A molecular phylogeny of the subtribe Pterostylidinae (Orchidaceae): resolving the taxonomic confusion

2010 ◽  
Vol 23 (4) ◽  
pp. 248 ◽  
Author(s):  
Jasmine K. Janes ◽  
Dorothy A. Steane ◽  
René E. Vaillancourt ◽  
Marco F. Duretto
Keyword(s):  
Bayesian Methods ◽  
Phylogenetic Trees ◽  
Taxonomic Status ◽  
Its Region ◽  
Population Level ◽  
Molecular Techniques ◽  
The Past ◽  
Single Well ◽  
Single Genus ◽  
Taxonomic Confusion

In the past decade, two major classification schemes of the subtribe Pterostylidinae have resulted in taxonomic confusion because a single well known genus was split into a large number of new genera and subgenera, many of which are difficult to discriminate accurately. These classifications have not been accepted widely among systematists because of poor phylogenetic support for several genera. Analyses of the internal transcribed spacer (ITS) region of nuclear rDNA in a large number of species and samples facilitate further clarification of the relationships within the Pterostylidinae. The phylogenetic trees were reconstructed using parsimony and Bayesian methods. These phylogenetic trees indicate that subtribe Pterostylidinae is monophyletic, and support the concept of a single genus, Pterostylis R.Br. sensu lato within the Pterostylidinae. Two clades representing subgenera correlate with the morphology of the lateral sepals, whereas several of the previously erected genera consistently have poor support. The proposed subgenera are divided further into 10 sections. Several closely related taxa with identical ITS sequences require further scrutiny by population-level molecular techniques to determine their taxonomic status.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Translating Molecular Profiling of Soft Tissue Sarcomas into Daily Clinical Practice

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 512
Author(s):  
Celine Jacobs ◽  
Lore Lapeire
Keyword(s):  
Soft Tissue ◽  
Unmet Need ◽  
Soft Tissue Sarcomas ◽  
Molecular Profiling ◽  
Point Of View ◽  
Molecular Techniques ◽  
Mesenchymal Tumors ◽  
The Past ◽  
Cancer Types ◽  
Sarcoma Treatment

Soft tissue sarcomas are a group of rare mesenchymal tumors with more than 70 subtypes described. Treatment of these subtypes in an advanced setting is mainly according to a one-size-fits-all strategy indicating a high unmet need of new and more targeted therapeutic options in order to optimize survival. The introduction of advanced molecular techniques in cancer has led to better diagnostics and identification of new therapeutic targets, leading to more personalized treatment and improved prognosis for several cancer types. In sarcoma, a likewise evolution is seen, albeit at a slower pace. This manuscript describes how in the past years advanced molecular profiling in soft tissue sarcomas was able to identify specific and often pathognomonic aberrations, deferring standard sarcoma treatment in favor of more targeted treatment from an oncologist’s point of view.

scholarly journals Biosorption potential and molecular characterization of metal resistant autochthonous microbes from tannery solid waste

2021 ◽  
Author(s):  
Hajira Younas ◽  
Aisha Nazir ◽  
Zakia Latif ◽  
Janice E Thies ◽  
Muhammad Shafiq ◽  
...  
Keyword(s):  
Solid Waste ◽  
Its Region ◽  
Metal Resistance ◽  
Molecular Techniques ◽  
Bacterial Strains ◽  
Fungal Strains ◽  
Resistant Strains ◽  
Tannery Solid Waste ◽  
Clean Metal

This study encompasses isolation and screening of heavy metal-resistant fungal and bacterial strains from tannery solid waste (TSW). Twelve fungal strains and twenty-five bacterial strains were isolated from TSW. The growth of fungal strains was observed against different heavy metals ranging from 10 mg L -1 to 1050 mg L -1 and the growth of bacteria was observed in metal concentrations ranging from 10 mg L -1 to 1200 mg L -1 . Five multi-metal resistant fungal isolates belonging to the genus Trichoderma and ten bacterial isolates belonging to the genus Bacillus showed good metal resistance and biosorption potential. They were identified through molecular techniques, fungi based on ITS region ribotyping, and bacteria based on 16S rRNA ribotyping. The fungal strains were characterized as T. hamatum (TSWF-06), T. harzianum (TSWF-11), T. lixii (TSWF-02) and T. pseudokoningii (TSWF-03, TSWF-10). The bacterial strains were characterized as Bacillus xiamenensis (TSW-02), B. velezensis (TSW-05), B. piscis (TSW-06), B. safensis (TSW-10), B. subtilis (TSW-14, TSW-15, TSW-17) B. licheniformis (TSW-19), B. cereus (TSW-20) and B. thuringiensis (TSW-22). The fungal strains namely, T. pseudokoningii (TSWF-03) and T. harzianum proved to be two multi-metal resistant strains with good biosorption efficiency. Unlike fungi, bacterial strains showed metal specific resistance. The strains Bacillus xiamenensis , B. subtilis (TSW-14) and B. subtilis (TSW-15) showed good biosorption efficiency against Cr, B. safensis against Cu, B. piscis and B. subtilis (TSW-17) against Pb and B. licheniformis and B. thuringiensis against Zn. The autochthonous fungal and bacterial strains can therefore be employed to clean metal contaminated environments.

scholarly journals Characterization of Five New Earthworm Mitogenomes (Oligochaeta: Lumbricidae): Mitochondrial Phylogeny of Lumbricidae

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 580
Author(s):  
Hongyi Liu ◽  
Yufeng Zhang ◽  
Wei Xu ◽  
Yu Fang ◽  
Honghua Ruan
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Phylogenetic Studies ◽  
Octolasion Tyrtaeum ◽  
Eisenia Nordenskioldi ◽  
Novel Strategy

Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae.

scholarly journals GENETIC IDENTIFICATION OF AQUATIC INVERTEBRATES OF KAZAKHSTAN AS INDICATORS OF ORGANIC POLLUTANTS

2018 ◽  
pp. 139-148
Author(s):  
Alexandr Anatoljevich Volkov ◽  
Larisa Anatoljevna Kovaljova ◽  
Tatjana Timofeevna Troshina ◽  
Zhanara Omirbekovna Mazhibaeva ◽  
Dmitrij Valerjevich Pilin ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Trees ◽  
Aquatic Invertebrates ◽  
Species Abundance ◽  
Ecological Status ◽  
Taxonomic Status ◽  
Organic Pollution ◽  
Water Bodies ◽  
Genetic Identification ◽  
Morphological Identity

The article deals with carrying out DNA barcoding of aquatic invertebrates of Kazakhstan to identify their taxonomic status as organic pollution indicators. 33 species of the Balkhash-Alakol basin and the Zhayik river were analyzed. 21 species correlate (95-100%) with previously published sequences of invertebrates with well-known classifications in the GenBank and BOLD databases. The taxonomic discrepancy in morphometric and genetic parameters in certain species has been revealed. The discrepancy may be caused by the morphological identity in chironomids at a larval stage. The phylogenetic trees of the investigated species within the families Chironomidae and Moinidae have been indicated. Chironomids are represented by ten clades of different types of genetic polymorphism of DNA gene. Genetic links of Moinidae are detected in four groups including a cryptic species from Lake Alakol. It has been stated that in distribution of cryptic taxons in Moina family factors of salinity and depth of the lake are important, as well as differences in depth. Molecular DNA-barcoding of invertebrates of Kazakhstan should be continued with covering a greater number of species and several replications, with qualified primary fixation of subjects of research and a sufficient number of samples. Authenticity of composition defining, species abundance, species characteristics of aquatic invertebrates from the water bodies of poorly explored arid regions is necessary for using them as indicators of the ecological status of water bodies.

scholarly journals Monitoring and risk assessment for groundwater sources in rural communities of Romania (GROUNDWATERISK)

2019 ◽  
Vol 5 ◽  
Author(s):  
Oana Teodora Moldovan ◽  
Rannveig Øvrevik Skoglund ◽  
Horia Leonard Banciu ◽  
Alexandra Dinu Cucoș ◽  
Erika Andrea Levei ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Drinking Water ◽  
Rural Communities ◽  
Groundwater Resources ◽  
Molecular Techniques ◽  
The Past ◽  
Physico Chemical ◽  
Groundwater Ecosystems ◽  
Alternative Sources ◽  
Agricultural Areas

In the past 100 years, a decreasing rainfall trend has been recorded on Romanian territory, a trend that continues today. Therefore, realistic estimation of the groundwater resources is crucial, especially for the rural communities lacking the economic power to use alternative sources of drinking water. The groundwater sources used by rural communities in Romania generally originate directly from caves, wells or springs with no proper evaluation of the water quality. Groundwater is exposed to different pollutants, as bats' guano in caves, fertilizers in agricultural areas or livestock (cattle, sheep, goats, etc.) farms on the surface. On the other hand, the water extracted directly from inside the caves is affecting groundwater ecosystems, highly vulnerable to any human impact and neglected by European legislation so far. The project aims to monitor, during two consecutive years, groundwater sources with different degrees of above- and underground pollution, from different regions of Romania. To achieve the goals of the project, a multidisciplinary monitoring strategy that will include measurements of hydrological, physico-chemical and biological (microbiology and aquatic invertebrates’ assessment) parameters alongside the quantification of radon and stable isotopes, rainfall or possible inflows of water. The specific outcomes of this project are: i) to test, develop and validate a new, more rapid and efficient method for monitoring and risk assessment of groundwater sources – and not only – by using molecular techniques, and propose this method to the water agencies in Romania; ii) to propose for Romanian authorities to implement a harmonized coherent methodology to measure radon concentration in water, as a consequence of EURATOM Directive; and iii) to educate local communities that are using groundwater as source for drinking water and raise young people’s awareness on the benefits of ecosystem services provided by the groundwater.

Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively

2010 ◽  
Vol 60 (4) ◽  
pp. 963-971 ◽  
Author(s):  
Rafael R. de la Haba ◽  
Cristina Sánchez-Porro ◽  
M. Carmen Márquez ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The Family ◽  
23S Rrna Gene ◽  
Single Genus ◽  
Type Strains

We have carried out a polyphasic taxonomic characterization of the type strains of the species with the recently validated name Salinicola socius, together with two species that were phylogenetically closely related, Halomonas salaria and Chromohalobacter salarius. 16S rRNA gene sequence analyses showed that they constituted a coherent cluster, with sequence similarities between 98.7 and 97.7 %. We have determined the almost complete 23S rRNA gene sequences of these three type strains, and the percentage of similarity between them was 99.2–97.6 %. Phylogenetic trees based on the 16S rRNA and 23S rRNA gene sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a cluster separated from the other species of the genera of the family Halomonadaceae, supporting their placement in a single genus. All three species have ubiquinone 9 as the major respiratory quinone, and showed similar fatty acid and polar lipid profiles. The level of DNA–DNA hybridization between Salinicola socius DSM 19940T, Halomonas salaria DSM 18044T and Chromohalobacter salarius CECT 5903T was 41–21 %, indicating that they are different species of the genus Salinicola. A comparative phenotypic study of these strains following the proposed minimal standards for describing new taxa of the family Halomonadaceae has been carried out. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data we have emended the description of the species Salinicola socius and we propose to transfer the species Halomonas salaria and Chromohalobacter salarius to the genus Salinicola, as Salinicola salarius comb. nov. (type strain M27T =KCTC 12664T =DSM 18044T) and Salinicola halophilus nom. nov. (type strain CG4.1T =CECT 5903T =LMG 23626T), respectively.

scholarly journals Gyrodactylus magadiensis n. sp. (Monogenea, Gyrodactylidae) parasitising the gills of Alcolapia grahami (Perciformes, Cichlidae), a fish inhabiting the extreme environment of Lake Magadi, Kenya

Parasite ◽  
2019 ◽  
Vol 26 ◽  
pp. 76
Author(s):  
Quinton Marco Dos Santos ◽  
John Ndegwa Maina ◽  
Annemariè Avenant-Oldewage
Keyword(s):  
New Species ◽  
Cichlid Fish ◽  
Soda Lake ◽  
Its Region ◽  
Extreme Environment ◽  
Molecular Techniques ◽  
Diurnal Fluctuation ◽  
Lake Magadi ◽  
A New Species ◽  
Alcolapia Grahami

A new species of Gyrodactylus von Nordmann, 1832 is described from the gills of Alcolapia grahami, a tilapian fish endemic to Lake Magadi. This alkaline soda lake in the Rift Valley in Kenya is an extreme environment with pH as high as 11, temperatures up to 42 °C, and diurnal fluctuation between hyperoxia and virtual anoxia. Nevertheless, gyrodactylid monogeneans able to survive these hostile conditions were detected from the gills the Magadi tilapia. The worms were studied using light microscopy, isolated sclerites observed using scanning electron microscopy, and molecular techniques used to genetically characterize the specimens. The gyrodactylid was described as Gyrodactylus magadiensis n. sp. and could be distinguished from other Gyrodactylus species infecting African cichlid fish based on the comparatively long and narrow hamuli, a ventral bar with small rounded anterolateral processes and a tongue-shaped posterior membrane, and marginal hooks with slender sickles which are angled forward, a trapezoid to square toe, rounded heel, a long bridge prior to reaching marginal sickle shaft, and a long lateral edge of the toe. The species is also distinct from all other Gyrodactylus taxa based on the ITS region of rDNA (ITS1–5.8s–ITS2), strongly supporting the designation of a new species. These findings represent the second record of Gyrodactylus from Kenya, with the description of G. magadiensis bringing the total number of Gyrodactylus species described from African cichlids to 18.

scholarly journals Morphological and molecular identification of ectomycorrhizal fungi associated with Persian oak (Quercus brantii Lindl.) tree

2020 ◽  
Vol 66 (No. 6) ◽  
pp. 244-251
Author(s):  
Behnaz Yousefshahi ◽  
Masoud Bazgir ◽  
Samad Jamali ◽  
Fatemeh Valizadeh Kakhki
Keyword(s):  
Its Region ◽  
Molecular Techniques ◽  
Molecular Methods ◽  
Morphological Identification ◽  
Tree Roots ◽  
Microscopic Features ◽  
Zagros Zone ◽  
Oak Tree ◽  
Ecm Fungi ◽  
Quercus Brantii

Identification of ectomycorrhizal (ECM) fungi in different ecosystems has major significance. In this research, to identity ECM fungi, we used two methods including the morphological method and the molecular method that is more precise. Basidiocarp collection of fungi associated with oak tree (Quercus brantii Lindl.) roots was carried out in the spring season 2016 and was identified by morphological and molecular methods. We also checked macroscopic and microscopic features and measured each structure using BioloMICS Measures software. To verify the morphological identification, the internal transcribed spacer (ITS) region was amplified by PCR using the primer pair ITS1/ITS4, and the sequences were analyzed. According to the morphological observations, the identified species were Amanita crocea, Boletus comptus, Tricholoma giganteum, and Inocybe rimosa. Besides, based on molecular techniques by comparing sequences, we identified five species out of the eight ones as A. crocea and other species as T. giganteum, I. rimosa and B. comptus. Both morphological and molecular methods are necessary for identifying ECM fungi associated with tree roots in the Zagros zone in the west of Iran.

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