Molecular identification based on ITS sequences for Kappaphycus and Eucheuma cultivated in China

2011 ◽  
Vol 29 (6) ◽  
pp. 1287-1296 ◽  
Author(s):  
Sufen Zhao ◽  
Peimin He
Keyword(s):  
Molecular Identification ◽  
Its Sequences

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 The UNITE Database for Molecular Identification and for Communicating Fungal Species

2019 ◽  
Vol 3 ◽  
Author(s):  
Urmas Kõljalg ◽  
Kessy Abarenkov ◽  
R. Henrik Nilsson ◽  
Karl-Henrik Larsson ◽  
Andy F.S. Taylor
Keyword(s):  
Molecular Identification ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Fungal Species ◽  
Its Sequences ◽  
Current Version ◽  
Community Members ◽  
Global Biodiversity Information Facility ◽  
Unique System ◽  
Fungal Sequence

UNITE (https://unite.ut.ee; Nilsson et al. 2018) is an international community of scientists and citizen scientists established in 2001. The ambition of UNITE is to develop: 1) datasets and tools for robust and reproducible molecular identification; 2) Persistent Identifiers based system for the communicating fungal species. Datasets of the nuclear ribosomal internal transcribed spacer (ITS) region, form the basis for UNITE. The current version includes nearly 1 million public fungal ITS sequences. Datasets are curated and annotated by community members. During the past 15 years, they made more than 275 000 improvements. In the complete absence of Latin names for species, UNITE offers a unique system where species hypotheses (SH) are provided with Digital Object Identifiers (DOIs). The current version 8 of UNITE offers more than 800 000 DOI-based SHs. One such SH DOI page is shown in Fig. 1. These DOI identifiers are also incorporated into the taxonomic backbone, making communication of taxa seamless in both directions. DOI identifiers of species hypotheses are also used by GBIF (Global Biodiversity Information Facility) in order to publish high-throughput sequencing taxon occurrence data in their data portal. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include ITS-based species hypotheses for all eukaryotes and aggregation of full-length, high-quality ITS sequences generated by the PacBio Sequel system (https://www.pacb.com/products-and-services/sequel-system) from diverse material samples.

scholarly journals Molecular identification of Fusarium spp. isolated from tomato plant in Iraq and China

2017 ◽  
Vol 30 (1) ◽  
pp. 65-72
Author(s):  
Mohammed A. Fayyadh ◽  
Adnan I. Al-Badran ◽  
Iman S. Al-Jaafari
Keyword(s):  
Fusarium Oxysporum ◽  
Molecular Identification ◽  
Growth Pattern ◽  
Tomato Plant ◽  
Morphological Characteristics ◽  
Sensitivity Test ◽  
Its Sequences ◽  
Fusarium Spp

This study was conducted to identify Fusarium spp. isolated from tomato plant in Iraq and China. A total of 12 isolates from Iraq (1-12) and four isolates from China (M1-M4) were used in this study. Based on Morphological characteristics (color, growth pattern, Macro and Micro-conidia shape) high differences between Fusarium isolates were found. Sensitivity test to the fungicide carbendazim revealed that one third of isolates(4/12) from Iraq had EC50 values over than 1000?g/ml indicated that many Iraqi isolates have developed resistance to carbendazim. Based on ITS sequences, Fusarium isolates were identified as follow, isolates 1, 3, 5, 6, 7, 10 were identified as Fusarium oxysporum, isolates 8, 11 as F. solani, isolates 12, M1 and M3 as F. moniliforme, isolates 2, M2 and M4 as F. proliferatum, F. chlamydosporum and F. kyushuense , respectively.

Electron microscopy in diagnostic virology

1984 ◽  
Vol 42 ◽  
pp. 70-73
Author(s):  
S. E. Miller
Keyword(s):  
Electron Microscopy ◽  
Tissue Culture ◽  
Molecular Identification ◽  
Point Of View ◽  
Negative Stain ◽  
Viral Diagnosis ◽  
Electron Microscopist ◽  
Diagnostic Virology

The techniques for detecting viruses are many and varied including FAT, ELISA, SPIRA, RPHA, SRH, TIA, ID, IEOP, GC (1); CF, CIE (2); Tzanck (3); EM, IEM (4); and molecular identification (5). This paper will deal with viral diagnosis by electron microscopy and will be organized from the point of view of the electron microscopist who is asked to look for an unknown agent--a consideration of the specimen and possible agents rather than from a virologist's view of comparing all the different viruses. The first step is to ascertain the specimen source and select the method of preparation, e. g. negative stain or embedment, and whether the sample should be precleared by centrifugation, concentrated, or inoculated into tissue culture. Also, knowing the type of specimen and patient symptoms will lend suggestions of possible agents and eliminate some viruses, e. g. Rotavirus will not be seen in brain, nor Rabies in stool, but preconceived notions should not prejudice the observer into missing an unlikely pathogen.

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