Evaluation of the internal transcribed spacer 2 (ITS2) as a molecular marker for phylogenetic inference using sequence and secondary structure information in blow flies (Diptera: Calliphoridae)

Genetica ◽  
2011 ◽  
Vol 139 (9) ◽  
pp. 1189-1207 ◽  
Author(s):  
M. A. T. Marinho ◽  
A. C. M. Junqueira ◽  
A. M. L. Azeredo-Espin
Keyword(s):  
Secondary Structure ◽  
Molecular Marker ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Inference ◽  
Secondary Structure Information ◽  
Blow Flies ◽  
Structure Information ◽  
Internal Transcribed Spacer 2

scholarly journals Bali Bananas (Musa spp. L.) Genetic Relationship Based on Internal Transcribed Spacer 2 (ITS-2)

2020 ◽  
Vol 43 (4) ◽  
Author(s):  
Fenny Martha Dwivany ◽  
Muhammad Rifki Ramadhan ◽  
Carolin Lim ◽  
Agus Sutanto ◽  
Husna Nugrahapraja ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Genetic Relationship ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Resolving Power ◽  
Structure Information ◽  
Musa Spp ◽  
Internal Transcribed Spacer 2 ◽  
B Genome ◽  
A Genome

Banana is one of the most essential commodities in Bali island. It is not only for nutrition sources but also for cultural and religious aspects. However, Bali banana genetic diversity has not been explored; therefore, in this study, we focused on its genetic relationship using a molecular approach. This research aimed to determine the genetic relationship of Bali banana cultivars using the internal transcribed spacer 2 (ITS-2) region as a molecular marker. A total of 39 banana samples (Musa spp. L.) were collected from Bali island. The ITS-2 DNA regions were then amplified and sequenced from both ends. ITS-2 sequences were predicted using the ITS2 Database (http://its2.bioapps.biozentrum.uni-wuerzburg.de/). The multiple sequences alignment was performed using ClustalX for nucleotide-based tree and LocARNA to provide the secondary structure information. Phylogenetic trees were constructed using neighbor-joining (Kimura-2-parameter model, 1,000 bootstrap). The result showed that two clades were formed, one clade was abundant in A genome (AA and AAA), and the other rich in the B genome (BB and ABB). This result suggested that cultivars that had similar genomic compositions tended to be grouped within the same clade and separated with different genomic compositions. This study gives perspectives that ITS-2 sequences in bananas are quite similar and differ much compared to other families. Secondary structure has been described to provide more robust resolving power in phylogenetic analysis.

DNA barcoding coupled with secondary structure information enhances Achyranthes species resolution

2020 ◽  
Vol 19 ◽  
pp. 100269
Author(s):  
Dewasya P. Singh ◽  
Amit Kumar ◽  
Vereena Rodrigues ◽  
Kamasamudra N. Prabhu ◽  
Amit Kaushik ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Dna Barcoding ◽  
Secondary Structure Information ◽  
Structure Information

VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy

2011 ◽  
Vol 52 (1) ◽  
pp. 41-56 ◽  
Author(s):  
Michael C. Brothers ◽  
Anna E. Nesbitt ◽  
Michael J. Hallock ◽  
Sanjeewa G. Rupasinghe ◽  
Ming Tang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Chemical Shift ◽  
Secondary Structure ◽  
Homology Model ◽  
Secondary Structure Information ◽  
Model Accuracy ◽  
Structure Information
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