scholarly journals Application of rps16 Intron and trnL-trnF Intergenic Spacer Sequences to Identify Rengas clone Riau

2017 ◽  
Vol 9 (2) ◽  
Author(s):  
Dewi Indriyani Roslim ◽  
Herman Herman
Keyword(s):  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Molecular Technique ◽  
Dna Barcodes ◽  
Query Cover ◽  
Blastn Analysis ◽  
Total Dna ◽  
Polymerase Chain ◽  
Relationship Of

<p>Rengas clone Riau has been identified using morphological characters and molecular technique with a <em>psbA-trnH</em> intergenic spacer, however, this method can only determine its taxonomic status at genus level, namely <em>Gluta</em> sp.  This study reports application two DNA barcodes, i.e. <em>rps16 </em>intron<em> </em>and <em>trnL-trnF</em> intergenic spacer, to identify Rengas clone Riau.  The methods included collection of the leaves from Kajuik Lake, total DNA isolation, electrophoresis, PCR (polymerase chain reaction), gel purification and sequencing.  The <em>rps16 </em>intron size was 659 bp and the <em>trnL-trnF </em>intergenic spacer was 527 bp. The BLASTn analysis showed that sequences of the <em>rps16 </em>intron and the <em>trnL-trnF </em>intergenic spacer of <em>Gluta</em> sp clone Riau had 100% similarity to those of <em>G. renghas </em>deposited in GenBank.  These results were supported by high max score, high total score, query cover = 100%, and E-value = 0.  The dendrograms also showed the closest relationship of <em>Gluta</em> sp clone Riau with <em>G. renghas </em>deposited in GenBank compared to other species of <em>Gluta</em>.  In conclusion, this study succeeded in identifying Rengas clone Riau as <em>Gluta renghas</em> by using sequences of the <em>rps16 </em>intron and the <em>trnL-trnF</em> intergenic spacer. A combination of DNA barcodes could be applied to identify various plants as long as the database for the DNA barcodes is available in public database such as GenBank. </p>

Molecular systematics and phylogeography of the genus Echinops (Compositae, Cardueae–Echinopsinae): focus on the Iranian centre of diversification

Phytotaxa ◽  
2017 ◽  
Vol 297 (2) ◽  
pp. 101 ◽  
Author(s):  
SOMAYEH MONTAZEROLGHAEM ◽  
ALFONSO SUSANNA ◽  
JUAN ANTONIO CALLEJA ◽  
VALIOLLAH MOZAFFARIAN ◽  
MOHAMMAD REZA RAHIMINEJAD
Keyword(s):  
Eastern Mediterranean ◽  
Eastern Mediterranean Region ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Molecular Dating ◽  
Ancestral Area ◽  
Close Relationship ◽  
Taxonomic Changes ◽  
High Level ◽  
Relationship Of

A molecular phylogeny of the genus Echinops (Asteraceae, Cardueae) based on plastid and nuclear markers is presented. The study focuses on the Iranian representatives of the genus, which constitute a larger part of Echinops. The Bayesian cpDNA tree resulted in a large polytomy. However, the Bayesian ITS tree displayed a well-resolved topology more compatible with the taxonomic treatment generally accepted in Echinops. An ITS network illustrates a close relationship of haplotypes. Mapping diagnostic morphological characters onto the ITS tree revealed a high level of homoplasy among the studied taxa. Except for the life cycle, all other morphological characters evolved many times among the clades and most of them appeared to be of low taxonomical value. Based on the nucleotide polymorphism and haplotypes, the taxonomic status of some taxa was evaluated. The independent status of E. sect. Phaeochaete was confirmed by molecular analyses and morphological characters. The paraphyletic nature of E. sect. Echinops was confirmed. As for the molecular dating, our results suggest that the genus evolved in the early Miocene but the main speciation events took place in the Pliocene-Pleistocene. The biogeographic results do not support any specific ancestral area for Echinops, yet the model states that its current diversity originated in the Irano-Turanian Region and the Eastern Mediterranean region. Some taxonomic changes are suggested, in the synonymy and placement of some taxa. 

Incorrect sequencing and taxon misidentification: an example in the Trichinella genus

2010 ◽  
Vol 84 (3) ◽  
pp. 336-339 ◽  
Author(s):  
G. Marucci ◽  
G. La Rosa ◽  
E. Pozio
Keyword(s):  
Intergenic Spacer ◽  
Morphological Characters ◽  
Internal Transcribed Spacers ◽  
5S Rrna ◽  
Lsu Rdna ◽  
Intergenic Spacer Region ◽  
Reference Centre ◽  
Polymerase Chain ◽  
Taxon Identification ◽  
Selection Of

AbstractMolecular analyses such as polymerase chain reaction (PCR) and sequencing are very useful for taxon identification, especially when morphological characters useful for identifying taxa are lacking. However, the use of molecular tools can be the source of taxon misidentification if they are not correctly applied and the results are not critically evaluated and compared with the literature and GenBank data. We describe a case of misidentification of a taxon of the genus Trichinella due to sequencing mistakes, lack of reference material and selection of a single molecular marker. A Trichinella sp. isolate from an Iranian wild boar (Sus scrofa) was identified as belonging to the Nearctic species Trichinella murrelli, through the molecular analysis of the 5S rRNA intergenic spacer region. A successive molecular identification of the same isolate was performed by the International Trichinella Reference Centre in Rome, Italy, using the 5S rRNA intergenic spacer region, the LSU rDNA expansion segment five, and the internal transcribed spacers 1 and 2. According to these analyses, the Iranian isolate belonged to Trichinella britovi, a Palaearctic species already described in Iran.

scholarly journals Confirmation of Tuntun Angin (Elaeocarpus floribundus) Taxonomic Status Using matK and ITS Sequences

2016 ◽  
Vol 8 (3) ◽  
pp. 393
Author(s):  
Dewi Indriyani Roslim ◽  
Siti Khumairoh ◽  
Herman Herman
Keyword(s):  
Molecular Identification ◽  
Intergenic Spacer ◽  
Biology Education ◽  
Taxonomic Status ◽  
Its Sequences ◽  
Morphological Identification ◽  
Its Sequence ◽  
Query Cover ◽  
Identification Techniques ◽  
Scientific Name

<p>Tuntun angin is one of important floodplain plants in and around Kajuik Lake located in Riau Province, Indonesia. Morphological identification shows that the scientific name of this plant is <em>Elaeocarpus floribundus. </em>The study aimed to confirm the taxonomic status of tuntun angin using <em>matK</em> and nuclear intergenic spacer (ITS) sequences. The methods included fresh leaf DNA isolation, polymerase chain reaction, electrophoresis, sequencing, and data analysis using BLASTn program and MEGA software version 6.06 programs. The results showed that the <em>matK</em> sequence (519 bp) of tuntun angin had highest similarity to <em>E. floribundus</em> <em>matK</em> sequence that was available in GenBank. It was supported by the high max score (937), low E-value (0.0), high identity value (100%), and high query cover (100%). However, the ITS sequence of tuntun angin did not show similarity to <em>E. floribundus </em>ITS sequence because there was no database of the sequence in GenBank. This study was able to confirm the taxonomic status of tuntun angin as <em>E. floribundus</em> using <em>matK</em> sequence and also showed that morphological and molecular identification techniques were complementary to each other. Moreover, this study enriched the DNA sequence database of <em>E. floribundus </em>in GenBank which will be useful for this species’ molecular identification.</p><p><strong>How to Cite</strong></p><p>Roslim, D. I., Khumairoh, S. &amp; Herman, H. (2016). Confirmation of Tuntun Angin (<em>Elaeocarpus floribundus</em>) Taxonomic Status Using <em>matK</em> and ITS Sequences. <em>Biosaintifika: Journal of Biology &amp; Biology Education</em>, 8(3), 393-400. </p>

scholarly journals Evidencia morfológica y molecular en la delimitación de Behria y Bessera, dos géneros del complejo Milla (Themidaceae)

2019 ◽  
Vol 85 ◽  
pp. 113
Author(s):  
Etelvina Gándara ◽  
Victoria Sosa ◽  
José Luis León De La Luz
Keyword(s):  
Baja California ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Volcanic Belt ◽  
Morphological Characters ◽  
Monotypic Genus ◽  
Diagnostic Characters ◽  
Mexican Volcanic Belt ◽  
The Pacific ◽  
Trans Mexican Volcanic Belt

Among the taxa of the <em>Milla</em> complex (Themidaceae), a monocot group of perennial petaloid geophytes, there are two genera with controversial taxonomic status: <em>Behria</em> andBessera. Tree-based and character-based analyses were conducted on 14 populations to determine if they should be considered different taxa. In addition, ecological separation was taken into account. As outgroups representative taxa of <em>Dandya, Jaimehintonia, Milla and Petronymphe,</em> i.e. the rest of the genera in the <em>Milla</em> clade, were used. <em>Behria</em> is a monotypic genus restricted to Baja California and <em>Bessera</em> includes two species from the Pacific slopes of Mexico and the Trans-Mexican Volcanic Belt. The chloroplast intergenic spacer <em>psbK-psbI</em> was sequenced and 37 morphological characters were coded. Tree-based analyses retrieved all populations of <em>Behria </em> and all populations of <em>Bessera</em> as monophyletic groups, both forming part of a more inclusive clade. Character-based analysis detected six diagnostic characters, all of which were floral. The conclusion of recognizing <em>Behria</em> and <em>Bessera</em> as independent genera was based on these results and also on their different distributional ranges.

scholarly journals Echinococcus granulosus from Mexican pigs is the same strain as that in Polish pigs

2007 ◽  
Vol 81 (3) ◽  
pp. 287-292 ◽  
Author(s):  
A. Cruz-Reyes ◽  
C.C. Constantine ◽  
A.C. Boxell ◽  
R.P. Hobbs ◽  
R.C.A. Thompson
Keyword(s):  
Echinococcus Granulosus ◽  
Fragment Length Polymorphism ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Taxonomic Status ◽  
Distinct Strain ◽  
Close Relationship ◽  
Sequencing Part ◽  
Polymerase Chain ◽  
Relationship Of

AbstractSamples of Echinococcus granulosus from seven pigs from Mexico were compared with isolates of the parasite from pigs in Poland and representative strains and species of Echinococcus. Isolates from pigs in Mexico were found to be genetically identical to E. granulosus from Polish pigs and distinct from other major genotypes by sequencing part of the mitochondrial cytochrome c oxidase I (COI) mtDNA locus, restriction fragment length polymorphism (RFLP) of the polymerase chain reaction (PCR) amplified rDNA internal transcribed spacer (ITS) 1 using five different enzymes, and random amplified polymorphic DNA (RAPD) analysis. These results were complemented by data on hook morphology and together strengthen the view that Echinococcus maintained in a cycle involving pigs and dogs is a distinct strain that is conserved genetically in different geographical areas. The present study supports the close relationship of the cervid, camel and pig strains and raises the question of their taxonomic status.

Notes on the molecular taxonomy of the Proclossiana eunomia complex (Lepidoptera, Nymphalidae: Argynnini): analysis of DNA barcodes

2018 ◽  
Vol 8 (1) ◽  
pp. 222-232 ◽  
Author(s):  
R. V. Yakovlev ◽  
N. A. Shapoval ◽  
G. N. Kuftina ◽  
A. V. Kulak ◽  
S. V. Kovalev
Keyword(s):  
Body Size ◽  
Molecular Taxonomy ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Coi Gene ◽  
Wing Pattern ◽  
Molecular Approach ◽  
Dna Barcodes ◽  
Morphological Differences ◽  
Proclossiana Eunomia

The Proclossiana eunomia (Esper, 1799) complex is currently composed of the several subspecies distributed throughout Palaearсtic region and North America. Despite the fact that some of the taxa have differences in wing pattern and body size, previous assumptions on taxonomy not supported by molecular data. Therefore, the identity of certain populations of this complex has remained unclear and the taxonomic status of several recently described taxa is debated. Here, we provide insights into systematics of some Palaearctic members of this group using molecular approach, based on the analysis of the barcoding fragment of the COI gene taking into account known morphological differences.

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 Characterization of Xanthomonas axonopodis pv. phaseoli isolates

2008 ◽  
Vol 34 (3) ◽  
pp. 228-231 ◽  
Author(s):  
Willian Mário de Carvalho Nunes ◽  
Maria Júlia Corazza ◽  
Silvana Aparecida Crestes Dias de Souza ◽  
Siu Mui Tsai ◽  
Eiko Eurya Kuramae
Keyword(s):  
Xanthomonas Campestris ◽  
Random Amplified Polymorphic Dna ◽  
Hypersensitive Reaction ◽  
Chain Reaction ◽  
Xanthomonas Axonopodis ◽  
Paulo State ◽  
Total Dna ◽  
Polymerase Chain ◽  
Bacterial Plant Pathogen

A simple, quick and easy protocol was standardized for extraction of total DNA of the bacteria Xanthomonas axonopodis pv. phaseoli. The DNA obtained by this method had high quality and the quantity was enough for the Random Amplified Polymorphic DNA (RAPD) reactions with random primers, and Polymerase Chain Reaction (PCR) with primers of the hypersensitivity and pathogenicity gene (hrp). The DNA obtained was free of contamination by proteins or carbohydrates. The ratio 260nm/380nm of the DNA extracted ranged from 1.7 to 1.8. The hrp gene cluster is required by bacterial plant pathogen to produce symptoms on susceptible hosts and hypersensitive reaction on resistant hosts. This gene has been found in different bacteria as well as in Xanthomonas campestris pv. vesicatoria (9). The primers RST21 and RST22 (9) were used to amplify the hrp gene of nine different isolates of Xanthomonas axonopodis pv. phaseoli from Botucatu, São Paulo State, Brazil, and one isolate, "Davis". PCR amplified products were obtained in all isolates pathogenic to beans.

Beyond Wallace: a new lineage of Chrysorthenches (Lepidoptera: Yponomeutoidea: Glyphipterigidae) reveals a journey tracking its host-plants, Podocarpus (Pinopsida: Podocarpaceae)

2020 ◽  
Vol 190 (2) ◽  
pp. 709-736
Author(s):  
Jae-Cheon Sohn ◽  
Shigeki Kobayashi ◽  
Yutaka Yoshiyasu
Keyword(s):  
Maximum Likelihood ◽  
East Asia ◽  
Host Plants ◽  
Morphological Characters ◽  
Species Group ◽  
Geological History ◽  
Dna Barcodes ◽  
History Of ◽  
Species Groups ◽  
Maximum Likelihood Phylogeny

Abstract A northward trans-Wallacean radiation is demonstrated for Chrysorthenches, a member of the Orthenches group. Here we review Chrysorthenches and allied genera resulting in a generic transfer of Diathryptica callibrya to Chrysorthenches and two new congeners: C. muraseaeSohn & Kobayashisp. nov. from Japan and C. smaragdinaSohnsp. nov. from Thailand. We review morphological characters of Chrysorthenches and allied genera, and find polyphyly of Diathryptica and the association of the Orthenches-group with Glyphipterigidae. These findings were supported in a maximum likelihood phylogeny of DNA barcodes from ten yponomeutoids. We analysed 30 morphological characters for 12 species of Chrysorthenches, plus one outgroup, via a cladistic approach. The resulting cladogram redefined two pre-existing Chrysorthenches species-groups and identified one novel lineage: the C. callibrya species-group. We review the host associations between Chrysorthenches and Podocarpaceae, based on mapping the working phylogenies. Our review suggests that ancestral Chrysorthenches colonized Podocarpus and later shifted to other podocarp genera. Biogeographical patterns of Chrysorthenches show that they evolved long after the Podocarpaceae radiation. Disjunctive trans-Wallacean distribution of the C. callibrya species-group is possibly related to the tracking of their host-plants and the complicated geological history of the island-arc system connecting Australia and East Asia.

scholarly journals Easy and Efficient DNA Extraction from Woody Plants for the Detection of Phytoplasmas by Polymerase Chain Reaction

Plant Disease ◽  
1999 ◽  
Vol 83 (5) ◽  
pp. 482-485 ◽  
Author(s):  
Margaret J. Green ◽  
Dan A. Thompson ◽  
Donald J. MacKenzie
Keyword(s):  
Polymerase Chain Reaction ◽  
Plant Material ◽  
Woody Plant ◽  
Leaf Roll ◽  
Chain Reaction ◽  
Efficient Procedure ◽  
Identical Manner ◽  
Total Dna ◽  
Polymerase Chain ◽  
Selection Of

A simple and efficient procedure for the extraction of high-quality DNA from phytoplasma-infected woody and herbaceous plants for polymerase chain reaction (PCR) detection is described. This procedure does not require phenol, chloroform, or alcohol for the precipitation of nucleic acids. Herbaceous and woody plant material are extracted in an identical manner with no additional purification or enrichment steps required. The method utilizes commercially available microspin-column matrices, and the extraction of total DNA can be achieved in less than 1 h. The method has been used to successfully purify phytoplasma DNA from whole leaves, leaf petioles and midribs, roots, and dormant wood from a diverse selection of plant material. The phytoplasmas detected by PCR include pear decline, western X-disease, peach yellow leaf roll, peach rosette, apple proliferation, Australian grapevine yellows, and Vaccinium witches'-broom.

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