Internal transcribed spacer sequence based identification and phylogenic relationship of Herba Dendrobii

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
C.-T. Wu ◽  
S.K. Gupta ◽  
A.Z.-M. Wang ◽  
S.-F. Lo ◽  
C.-L. Kuo ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenic Relationship ◽  
Relationship Of

Phylogenetic position of Arabis arenicola and generic limits of Aphragmus and Eutrema (Brassicaceae) based on sequences of nuclear ribosomal DNA

2006 ◽  
Vol 84 (2) ◽  
pp. 269-281 ◽  
Author(s):  
Suzanne I. Warwick ◽  
Ihsan A. Al-Shehbaz ◽  
Connie A. Sauder
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
New Combinations ◽  
Arabidopsis Lyrata ◽  
Relationship Of

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 45 taxa were used to determine the phylogenetic relationship of Arabis arenicola to Arabis , Arabidopsis , Braya , and Eutrema , and that of Eutrema to the purportedly related genera Aphragmus , Lignariella , Neomartinella , Platycraspedum , Taphrospermum , and Thellungiella . Arabis arenicola was originally described as Eutrema in 1830, transferred to Arabis in 1898, and has remained in Arabis to the present, even though it is morphologically more similar to Arabidopsis, Braya, and Eutrema. Sequence data were obtained from representative taxa of Arabis, Arabidopsis, and related Boechera and Catolobus, Braya and Neotorularia, and Eutrema, Aphragmus, Lignariella, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. The five Arabis arenicola accessions examined had ITS sequences that were identical to each other and to four Arabidopsis lyrata accessions. In both maximum parsimony and maximum likelihood analyses, Arabis arenicola fell within the Arabidopsis clade and was closely aligned with Arabidopsis lyrata. Two of six purportedly related genera were not closely related to Eutrema. Both analyses placed Lignariella within a separate well-supported clade with Aphragmus, while the other four genera, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella, fell within a well-supported clade with Eutrema. Morphology and molecular data strongly suggest transferring Arabis arenicola to Arabidopsis, expanding Aphragmus to include Lignariella, and expanding Eutrema to include Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. New combinations in Arabidopsis and Aphragmus are proposed.

scholarly journals The systematic position of Gradsteinia andicola Ochyra (Donrichardsiaceae, Bryopsida) : evidence from nrDNA internal transcribed spacer sequences

2000 ◽  
Vol 18 (1) ◽  
pp. 75-85
Author(s):  
Michael Stech ◽  
Jan-Peter Frahm
Keyword(s):  
New Zealand ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Systematic Position ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Tree ◽  
Systematic Relationship ◽  
Parsimony Tree ◽  
Internal Transcribed Spacer Sequences ◽  
Relationship Of

Nuclear ribosomal DNA internal transcribed spacer (ITS) 1/2 sequences of the Colombian endemic Gradsteinia andicola were determined and compared with those of 16 other species of the Hypnales (Amblystegiaceae, Brachytheciaceae, Hypnaceae, Plagiotheciaceae and Rhytidiaceae). In a maximum parsimony tree Gradsteinia andicola belongs to a well supported clade consisting of Amblystegium, Cratoneuron, Cratoneuropsis, Hypnobartlettia and Palustriella, and seems to be closely related to Cratoneuropsis relaxa from New Zealand. Gradsteinia andicola is therefore transferred to Amblystegiaceae, but the genus Gradsteinia is maintained. The systematic relationship of Amblystegiaceae and Donrichardsiaceae is discussed.

Kinetic property and phylogenic relationship of 2-hydroxymuconic semialdehyde dehydrogenase encoded intomC gene ofBurkholderia cepacia G4

2004 ◽  
Vol 27 (5) ◽  
pp. 570-575
Author(s):  
Alavala Matta Reddy ◽  
Kyung Rak Min ◽  
Kyoung Lee ◽  
Jai Yun Lim ◽  
Chi-Kyung Kim ◽  
...  
Keyword(s):  
Kinetic Property ◽  
Semialdehyde Dehydrogenase ◽  
Phylogenic Relationship ◽  
Relationship Of

scholarly journals The Distribution of COVID 19 based on Phylogeny Construction in Silico Sequences SARS-CoV-2 RNA at Genbank NCBI

2020 ◽  
Vol 17 (8) ◽  
pp. 893-902
Author(s):  
Revolson Alexius MEGE ◽  
Herry Sinyo SUMAMPOUW ◽  
Dewa Nyoman OKA ◽  
Nonny MANAMPIRING ◽  
Yermia Semuel MOKOSULI
Keyword(s):  
In Silico ◽  
Gene Sequence ◽  
Evolutionary Relationship ◽  
Monophyletic Group ◽  
The World ◽  
Gene Database ◽  
Phylogenic Relationship ◽  
Human Viruses ◽  
Respiratory Coronavirus ◽  
Relationship Of

The Covid-19 pandemic, due to severe acute respiratory coronavirus (SARS-CoV-2) virus, has an effect on human civilization today. With high fatality infections, SARS Covid-19 has influenced the global economic, socio-cultural, and even political order. This study aims to construct the phylogeny of the SARS corona virus that causes Covid-19 in various countries in the world by using the SARS Covid-19 gene database from the NCBI GenBank. The results of this study can trace the origin of SARS Covid-19, which is then called SARS-CoV-2, the gene characteristics, and the evolutionary relationship of these genes to various countries in the world. This research uses in silico method with gene sequence sources from the NCBI GenBank (www.ncbi.nih.gov). A total of 433 SARS Covid-19 sequences reported by 21 countries as of April 2rd, 2020 were the subject of the study. Sequences representing each country were analyzed using the MEGA 7.0 program. The results showed that the phylogeny trees formed were obtained by 2 main monophyletic groups. The first major monophyletic group consisted of 11 nodes, with 19 SARS-CoV-2 gene sequences from 23 countries. The second major monophyletic group consisted of 5 nodes with 5 countries of origin of SARS-CoV sequence 19. The spread of Covid-19 from the epicenter in Wuhan, China to the world has taken place randomly. This has happened because of the migration of people from the Chinese epicenter. The location of the countries adjacent to China did not determine the closest phylogenic relationship. The number of phylogenetic nodes formed showed mutases which caused very high variations of the SARS CoV 2 RNA gene sequence. The results of this study reinforce that efforts to limit the spread of human viruses to humans must be done. The presence of sequences from China in the 2 main monophyletic groups confirms that this virus originated in the Chinese epicenter.

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