scholarly journals DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sonia Trujillo-Argueta ◽  
Rafael F. del Castillo ◽  
Daniel Tejero-Diez ◽  
Carlos Alberto Matias-Cervantes ◽  
Abril Velasco-Murguía
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Trees ◽  
Cloud Forest ◽  
Phylogenetic Analyses ◽  
Universal Primers ◽  
Sign Test ◽  
Species Discrimination ◽  
P Value ◽  
Interspecific Divergence ◽  
Forest Plants

AbstractDNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. rbcLa showed the highest species discrimination in BLASTn (66.67%). trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e−16). Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. ML trees showed the highest mean support value (80.95%). trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. Species discrimination did not increase using rbcLa + trnH-psbA. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.

scholarly journals Deciphering amphibian diversity through DNA barcoding: chances and challenges

2005 ◽  
Vol 360 (1462) ◽  
pp. 1859-1868 ◽  
Author(s):  
Miguel Vences ◽  
Meike Thomas ◽  
Ronald M Bonett ◽  
David R Vieites
Keyword(s):  
Dna Barcoding ◽  
Single Locus ◽  
Universal Primers ◽  
Nuclear Markers ◽  
Amphibian Species ◽  
Interspecific Divergence ◽  
Candidate Species ◽  
Mitochondrial Population ◽  
Tremendous Amount ◽  
Definition Of

Amphibians globally are in decline, yet there is still a tremendous amount of unrecognized diversity, calling for an acceleration of taxonomic exploration. This process will be greatly facilitated by a DNA barcoding system; however, the mitochondrial population structure of many amphibian species presents numerous challenges to such a standardized, single locus, approach. Here we analyse intra- and interspecific patterns of mitochondrial variation in two distantly related groups of amphibians, mantellid frogs and salamanders, to determine the promise of DNA barcoding with cytochrome oxidase subunit I ( cox1 ) sequences in this taxon. High intraspecific cox1 divergences of 7–14% were observed (18% in one case) within the whole set of amphibian sequences analysed. These high values are not caused by particularly high substitution rates of this gene but by generally deep mitochondrial divergences within and among amphibian species. Despite these high divergences, cox1 sequences were able to correctly identify species including disparate geographic variants. The main problems with cox1 barcoding of amphibians are (i) the high variability of priming sites that hinder the application of universal primers to all species and (ii) the observed distinct overlap of intraspecific and interspecific divergence values, which implies difficulties in the definition of threshold values to identify candidate species. Common discordances between geographical signatures of mitochondrial and nuclear markers in amphibians indicate that a single-locus approach can be problematic when high accuracy of DNA barcoding is required. We suggest that a number of mitochondrial and nuclear genes may be used as DNA barcoding markers to complement cox1 .

scholarly journals Research on Phylogenetic Relationship of Lotus Populations Collected in Thua Thien Hue Province, Vietnam based on the Chloroplast Genome by DNA Barcode

2021 ◽  
Author(s):  
Dang Thanh Long ◽  
Hoang Thi Kim Hong ◽  
Le Ly Thuy Tram ◽  
Nguyen Thi Quynh Trang
Keyword(s):  
Chloroplast Genome ◽  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Haplotype Diversity ◽  
Universal Primers ◽  
Nucleotide Position ◽  
Accurate Identification ◽  
Low Levels ◽  
Relationship Of

Background: The DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. Methods: DNA barcoding of 9 chloroplast genes (rbcL, matK, trnH-psbA, accD-psaI, ndhA, psbE-petL, Rpl32-trnL, trnW-psaJ, trnSGCU-trnGGCC) were used to provide the theoretical basis for species identification, genetic diversity analysis of lotus population collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequence products were analyzed using the MEGA X program. Result: The results showed that high levels of haplotype diversity (Hd), ranging from 0.618-0.869 and low levels of nucleotide diversity (Pi), ranging from 0.180 × 10-3-3.280 × 10-3 base on a total of nine gene regions of chloroplast genome. The neutrality tests show an excess of rare nucleotide position variations in individuals’ white lotus and derived haplotypes recent expansion. While the evolution of the individuals in the pink lotus may have to decrease. The phylogenetic analyses indicated that combined sequences were not insufficient to make a difference to the DNA barcoding in the individual’s lotus of the N. nucifera species this is in the study. The standardized and accurate barcode information of lotus is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Nelumbonaceae germplasm resources.

Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

2021 ◽  
Author(s):  
Sonexay Rasphone ◽  
Long Thanh Dang ◽  
Hoan Nguyen ◽  
Ngoc Quang Nguyen ◽  
Oanh Thi Duong ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Maximum Likelihood Method ◽  
Dna Barcode ◽  
Population Expansion ◽  
Nuclear Ribosomal Dna ◽  
Likelihood Method ◽  
Gene Region ◽  
Universal Primers ◽  
Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals Genome-scale reconstructions to assess metabolic phylogeny and organism clustering

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0240953
Author(s):  
Christian Schulz ◽  
Eivind Almaas
Keyword(s):  
Phylogenetic Trees ◽  
Metabolic Networks ◽  
Sulfur Metabolism ◽  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Significant Heterogeneity ◽  
Metabolic Reaction ◽  
High Quality ◽  
Conserved Genes ◽  
Genome Scale

Approaches for systematizing information of relatedness between organisms is important in biology. Phylogenetic analyses based on sets of highly conserved genes are currently the basis for the Tree of Life. Genome-scale metabolic reconstructions contain high-quality information regarding the metabolic capability of an organism and are typically restricted to metabolically active enzyme-encoding genes. While there are many tools available to generate draft reconstructions, expert-level knowledge is still required to generate and manually curate high-quality genome-scale metabolic models and to fill gaps in their reaction networks. Here, we use the tool AutoKEGGRec to construct 975 genome-scale metabolic draft reconstructions encoded in the KEGG database without further curation. The organisms are selected across all three domains, and their metabolic networks serve as basis for generating phylogenetic trees. We find that using all reactions encoded, these metabolism-based comparisons give rise to a phylogenetic tree with close similarity to the Tree of Life. While this tree is quite robust to reasonable levels of noise in the metabolic reaction content of an organism, we find a significant heterogeneity in how much noise an organism may tolerate before it is incorrectly placed in the tree. Furthermore, by using the protein sequences for particular metabolic functions and pathway sets, such as central carbon-, nitrogen-, and sulfur-metabolism, as basis for the organism comparisons, we generate highly specific phylogenetic trees. We believe the generation of phylogenetic trees based on metabolic reaction content, in particular when focused on specific functions and pathways, could aid the identification of functionally important metabolic enzymes and be of value for genome-scale metabolic modellers and enzyme-engineers.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals Phylogenetic analysis of canine parvoviruses from Turkey

2020 ◽  
Vol 76 (01) ◽  
pp. 6334-2020
Author(s):  
ZEYNEP AKKUTAY-YOLDAR ◽  
TAYLAN KOÇ B.
Keyword(s):  
High Mortality ◽  
Phylogenetic Trees ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Canine Parvovirus ◽  
Mortality And Morbidity ◽  
Identity Match ◽  
Genomic Characterization

Canine parvovirus (CPV) type 2 is the causative agent of acute hemorrhagic enteritis and high mortality in the affected dogs. Numerous studies have been done to understand the origin of the virus and to exhibit new variants and circulating strains. This report describes the detection and genomic characterization of CPV strains from indoor and outdoor dogs in Ankara, Turkey. Samples were sent to our laboratory due to clinical symptoms in puppies. We tested blood and swab samples to determine the presence of canine parvovirus (CPV) in three puppies and two adult dogs by reverse transcription-polymerase chain reaction (RT-PCR) using VP2 (capsid protein) region primers of canine parvoviruses. Following that, to provide molecular characterization data Maximum Likelihood (ML) method was used for phylogenetic analyses. Constructed phylogenetic trees from the aligned nucleotide sequences revealed that our CPV strains demonstrated high genetic similarities, with 100% identity match on nucleotide alignments with each other and classified in CPV-2b genotypes.They have placed on a monophyletic clade as a sister branch with CPV VAC S quantum with 98.9% nucleotide homology. Our findings suggest that CPV-2b is actual and frequently seen variant in Turkey and shows high similarities with other CPV variants and a bit less with FPVs in Turkey and around the world. CPV causes high mortality and morbidity in dogs and to develop effective vaccines for protection of dogs in Turkey where there are few numbers of studies that have been done, field strains should be isolated and characterised.

scholarly journals PENGARUH PELATIHAN DENGAN MODEL PEMBELAJARAN MAKE A MATCH TERHADAP KETERAMPILAN KADER POSYANDU DALAM MENGGUNAKAN BUKU KIA

2021 ◽  
Vol 7 (2) ◽  
pp. 53-58
Author(s):  
Dewi Zolekhah ◽  
Liberty Barokah ◽  
Elvika Fit Ari Shanti
Keyword(s):  
Sign Test ◽  
P Value ◽  
The One

Buku KIA merupakan buku yang berisi catatan kesehatan ibu dan anak yang dapat dijadikan sebagai pedoman dalam meningkatkan kualitas pelayanan kesehatan ibu dan anak melalui upaya mendeteksi secara dini adanya masalah kesehatan ibu dan anak. Kader diharuskan untuk membaca dan secara bertahap mempelajari buku KIA yang merupakan petunjuk nasional setelah mereka melakukan kegiatan Posyandu sebagai evaluasi atas apa yang telah mereka kerjakan. Terbatasnya informasi dan pelatihan kader yang kurang menyebabkan pengetahuan dan keterampilan kader tentang penggunaan buku KIA rendah. Tujuaan penelitian ini yaitu untuk mengetahui pengaruh pelatihan dengan model pembelajraan kooperatif terhadap keterampilan kader dalam menggunakan buku KIA. Jenis penelitian ini adalah pra eksperimental dengan rancangan (The One Group Pretest Posttest) dengan populasi 30 kader Posyandu sebagai sampel di wilayah kerja Puskesmas. Analisis data menggunakan Wilxocon Sign test, didapatkan p value (0,000) < 0,005. Hasil uji prasyarat parametrik untuk data keterampilan didapatkan data tidak berdistribusi normal, analisis data menggunakan wilcoxon, didapatkan hasil nilai p value 0,000 < 0,005 sehingga terdapat perbedaan yang bermakna keterampilan kader sebelum dan sesudah diberikan pelatihan dengan model pembelajaran kooperatif terhadap keterampilan kader posyandu  dalam menggunakan buku KIA.

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 Characterization and Phylogeny of Fungi from Industrial Wastewater Using Highly Conserved Multiple Gene Loci

2021 ◽  
Author(s):  
Blessing Amaka Ezeonuegbu ◽  
Dauda Abdullahi Machido ◽  
Clement Z. Whong ◽  
Wisdom S. Japhet ◽  
Clement Ameh Yaro ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Industrial Effluent ◽  
Pcr Amplification ◽  
Morphological Characterization ◽  
Likelihood Method ◽  
Internal Transcribed Spacer Region ◽  
Fungal Isolates ◽  
Fungal Dna Extraction

Abstract The aim of this study was isolation and molecular characterization of fungi from untreated industrial effluent by multigene phylogenetic analyses. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (Ben A), calmodulin (CaM), and DNA-directed RNA polymerase second large subunit (RPB2) genes, along with morphological characterization and species diversity. Fungal DNA extraction kits and primers sets for the selected genes were purchased and used following the manufacturer’s instructions. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. All the sequences from this study were deposited in GenBank and the accession number assigned. Phylogenetic trees of the fungal isolates were drawn for each gene by the Maximum Likelihood method using MEGA 7.0 software. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium and Trichoderma with Aspergillus as the predominant genus were identified.

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