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 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>

New species of the Lepraria neglecta group (Stereocaulaceae, Ascomycota) from Europe

2007 ◽  
Vol 39 (4) ◽  
pp. 319-327 ◽  
Author(s):  
Štěpánka SLAVÍKOVÁ-BAYEROVÁ ◽  
Judith FEHRER
Keyword(s):  
Fatty Acids ◽  
New Species ◽  
Central Europe ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Its Sequences ◽  
Its Sequence ◽  
Core Group ◽  
A New Species

Abstract:Lepraria granulata Slavíková, a new species from Eastern and Central Europe, is described. According to its morphology, ITS sequence and ecology, it belongs to the L. neglecta core group. Lepraria granulata is characterized by producing atranorin and two, so far unidentified, fatty acids (‘granulata unknown 1 & 2’) and phylogenetic analyses show that it is clearly distinguished from previously known species. Two additional taxa, provisionally named Lepraria sp. G and Lepraria sp. BG, are also discussed. According to their morphology and ITS sequences, they also belong to the L. neglecta group. Lepraria sp. G is sister to L. granulata whereas Lepraria sp. BG is basal and well separated from all taxa so far known in the group. Their taxonomic status is not yet entirely clear.

scholarly journals Identification of species of Abiotrophia, Enterococcus, Granulicatella and Streptococcus by sequence analysis of the ribosomal 16S–23S intergenic spacer region

2007 ◽  
Vol 56 (4) ◽  
pp. 504-513 ◽  
Author(s):  
Sheng Kai Tung ◽  
Lee Jene Teng ◽  
Mario Vaneechoutte ◽  
Hung Mo Chen ◽  
Tsung Chain Chang
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Identification ◽  
Intergenic Spacer ◽  
Its Sequences ◽  
Rrna Gene ◽  
Its Sequence ◽  
Its Sequencing ◽  
Intergenic Spacer Region

The feasibility of sequence analysis of the ribosomal 16S–23S intergenic spacer region (ITS) was evaluated for identification of 24 species of Streptococcus, one species of Abiotrophia, 18 species of Enterococcus and three species of Granulicatella. As GenBank currently lacks ITS sequence entries for many species of these four genera, the ITS sequences of 38 type strains were first sequenced and submitted to GenBank to facilitate species identification of these genera. Subsequently, the ITS sequences of 217 strains (84 reference strains and 133 clinical isolates) were determined and species identification was made by blast search for homologous sequences in public databases. Species other than Streptococcus contained multiple ITS fragments and only the shortest fragment was analysed. A total of 25 isolates (11.5 %) produced discrepant identification by ITS sequencing. The 25 discordant strains were analysed further by sequencing of the 16S rRNA gene for species clarification, and 21 were found to be identified correctly by ITS sequence analysis. The correct identification rate by ITS sequencing was 98.2 % (213/217). Several closely related enterococcal and streptococcal species/subspecies contained specific ITS signature sequences that were useful for differentiating these bacteria. In conclusion, ITS sequencing provides a useful approach towards identifying this group of pathogens on a molecular platform alongside 16S rRNA gene sequencing.

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 Molecular Identification of Ectomycorrhizal Mycelium in Soil Horizons

2003 ◽  
Vol 69 (1) ◽  
pp. 327-333 ◽  
Author(s):  
Renske Landeweert ◽  
Paula Leeflang ◽  
Thom W. Kuyper ◽  
Ellis Hoffland ◽  
Anna Rosling ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Sequence Similarity ◽  
Mineral Soil ◽  
Molecular Techniques ◽  
Root Tip ◽  
Root Tips ◽  
Soil Horizons ◽  
Novel Approach ◽  
Total Dna ◽  
Identification Techniques

ABSTRACT Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (≥99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had ≥98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.

Molecular Identification and Morphological Characterization of Ficus sp. (Moraceae) in Bogor Botanic Gardens

2021 ◽  
Vol 6 (1) ◽  
pp. 36-44
Author(s):  
Muhammad Rifqi Hariri ◽  
Peniwidiyanti Peniwidiyanti ◽  
Arifin Surya Dwipa Irsyam ◽  
Rina Ratnasih Irwanto ◽  
Irfan Martiansyah ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Morphological Characterization ◽  
Species Level ◽  
Herbarium Specimen ◽  
Morphological Observation ◽  
Its Sequence ◽  
Botanic Gardens ◽  
Molecular Approaches ◽  
Vegetative Characters

Ficus spp. belongs to the tribe Ficeae in the Moraceae family. Many members of this genus have been collected and grown in Bogor Botanic Gardens. There are 519 living collections of Ficus conserved since 1817, and 13 of them have not been identified until the species level. This research aimed to identify the Ficus sp. originated from Kaur Selatan (Bengkulu) using morphological and molecular approaches. Morphological characterization and herbarium specimen observation have been carried out to identify the Ficus sp. The molecular approach was conducted through DNA barcoding using ITS primer. The molecular identification using ITS sequence showed that Ficus sp. is Ficus crassiramea with 99.87% similarity to the sequence in NCBI. Morphological observation through herbarium specimen showed that there are 9 vegetative characters specific to Ficus crassiramea.

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.

Pseudodactylaria brevis sp. nov. from Thailand confirms the status of Pseudodactylariaceae

Phytotaxa ◽  
2018 ◽  
Vol 369 (4) ◽  
pp. 241 ◽  
Author(s):  
CHUAN-GEN LIN ◽  
ERIC H. C. MCKENZIE ◽  
DARBHE J. BHAT ◽  
JIAN-KUI LIU ◽  
KEVIN D. HYDE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Its Sequence ◽  
Morphological Comparison ◽  
Phylogenetic Placement ◽  
Data Analyses ◽  
The Status ◽  
A New Species

A new species, Pseudodactylaria brevis, is described, illustrated and compared with other Pseudodactylaria and Dactylaria-like taxa. Evidence for the new species is provided by morphological comparison and sequence data analyses. Pseudodactylaria brevis can be distinguished from other Pseudodactylaria and Dactylaria-like species by its short hyaline conidiophores and fusiform, 1-septate hyaline conidia. Phylogenetic analysis of LSU and ITS sequence data was carried out to determine the phylogenetic placement of the species and confirm the taxonomic status of Pseudodactylariaceae.

scholarly journals Molecular identification of original plants of Spica prunellae based on ITS sequence

2010 ◽  
Vol 4 (19) ◽  
pp. 1948-1953 ◽  
Author(s):  
Sun Xiao Qin ◽  
Wei Yang Lian ◽  
Wu Bao Cheng ◽  
Guo Jian Lin ◽  
Hang Yue Yu
Keyword(s):  
Molecular Identification ◽  
Its Sequence

Group I Intron Versus its Sequences in Phylogeny of Cetrarioid Lichens

1999 ◽  
Vol 31 (5) ◽  
pp. 441-449 ◽  
Author(s):  
Arne Thell
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Group I Intron ◽  
Ribosomal Genes ◽  
Its Sequences ◽  
Its Sequence ◽  
Ribosomal Rna Gene ◽  
18S Ribosomal Rna Gene ◽  
Group I

AbstractPhylogenetic trees based on group I intron sequences and on internal transcribed spacer (ITS) sequences of mycobiont ribosomal genes were calculated and compared. Eight cetrarioid and four non-cetrarioid species of the Parmeliaceae were compared. The phylogeny based on group I intron sequences is partly congruent with the ITS sequence phylogeny. Group I intron sequences are presumably less informative for infragenic studies. The introns have a length of 214–233 nucleotides, and differ at up to 33% of the bases between species. All introns analysed are located between the positions 1516 and 1517 of the fungal 18S ribosomal RNA gene. Cetrarioid lichens form a non-homogeneous group within the Parmeliaceae according to both group I intron and ITS sequences.

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