scholarly journals Molecular Characteristics of Cytochrome B for Mackerel Barcoding

2016 ◽  
Vol 19 (1) ◽  
pp. 9 ◽  
Author(s):  
Deden Yusman Maulid ◽  
Mala Nurilmala ◽  
Nurjanah Nurjanah ◽  
Hawis Maddupa
Keyword(s):  
Molecular Weight ◽  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Cytochrome B ◽  
Pcr Amplification ◽  
3D Modelling ◽  
Molecular Characteristics ◽  
Cyt B ◽  
Scomberomorus Commerson ◽  
King Mackerel

<p>Cytochrome b (cyt b) is one of the genes in mitochondrial DNA that is often used as a molecular<br />marker to identify species through DNA Barcoding. The aim of the present study was to investigate the<br />bioinformatic of cyt b that isolated from mackerel fish. PCR amplification showed the length of DNA cyt<br />b from king mackerel was 803 bp within purine 312 bp and pyrimidine 491 bp while Korean mackerel 791<br />bp within purine 316 bp and pyrimidine 475 bp. Phylogenetic analysis showed all sample join in mackerel<br />groups (Scomberomorus commerson and Scomberomorus koreanus). The Isoelectric point value of cyt b from<br />king mackerel is 6.38 and molecular weight is 29826.23; Korean mackerel are 8.67 and molecular weight is<br />29372.77. Hydrophaty plot showed cyt b of mackerel more hydrophobic. Based on 3D modelling both of<br />them have eight different sections showing by different colors.<br />Keywords: characteristic molecular, cytochrome b, Mackerel<br /><br /></p>

scholarly journals Phylogenetic Analysis of Mitochondrial Genes of Malaysian Tupaia Reveals Composite Species in Tupaia Glis

2021 ◽  
Vol 3 (1) ◽  
pp. 197-203
Author(s):  
Jayaraj Vijaya Kumaran ◽  
Ahmad Sofiman Othman ◽  
Shahrul-Anuar Mohd Sah ◽  
Seri Intan Mokhtar
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Mitochondrial Genes ◽  
Peninsular Malaysia ◽  
Universal Primers ◽  
Cyt B ◽  
Southern Thailand ◽  
Tupaia Glis

Recent morphometric analysis on T. glis in Peninsular Malaysia indicates that there were more than one morphotypes in this species. Thus this study attempts to examine this phenomenon using mitochondrial DNA sequences of Cyt b and CO1 genes. A total of 74 DNA sequences for both genes were generated using available universal primers. Samples from Southern Thailand were found to be misidentified as T. glis when in fact these samples clustered with T. belangeri while one T. tana from Borneo was miss-identified as T. minor. The phylogenetic trees showed that there are at least one confirmed morphotype of Tupaia (new Tupaia sp.) that have yet to be described. The results also showed that the separation of T. glis morphotype 1 and 11 were visible in the combined genes tree, congruent with the morphometric phylogeny but had poor phylogenetic support.

scholarly journals Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

2018 ◽  
Vol 20 (1) ◽  
pp. 17-22
Author(s):  
TETY HARTATIK ◽  
DWI NUR HAPPY HARIYONO ◽  
YUDI ADINATA
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Cytochrome B Gene ◽  
Cyt B ◽  
Gene Sequences ◽  
Cattle Breeds ◽  
Cyt B Gene

Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds.

Phylogenetic Affi nities of the Globodera pallida Inferred From the mtDNA cyt-b Gene Polymorphism

2014 ◽  
Vol 1 (2) ◽  
pp. 3-11
Author(s):  
L. Pylypenko ◽  
V. Blok ◽  
M. Phillips
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variability ◽  
Cytochrome B ◽  
Software Package ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Sources Of Resistance ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene

The mitochondrial cytochrome b gene marker was used to investigate the genetic variability of G. pallida populations of different origins and selection on three sources of resistance. Aim. To sequence the mitochon- drial gene cyt-b and to clarify its application as a genetic marker for intraspecifi c genetic diversity study, phylogenetic analysis and nematode virulence assessment. Methods. The cysts of nematodes were used as a source for DNA extraction. Polymerase chain reaction was performed using the specifi c primers of INRAcytbL and INRAcytbR, followed by the amplifi ed product sequencing. The nucleotide sequences were processed and aligned using software PhredPhrap, CONSED and Clustal W. MEGA-4, DNADIST software package; while PHYLIP and Arlequin were used for statistical analysis. Phylogenetic trees construction and visualization were performed using the software package PHYLIP and TREEVIEW. Results. The phylogenetic analysis based on mitochondrial cytochrome b gene sequences has showed that the Ukrainian populations of G. pallida were almost identical to other populations from the Europe. Limited genetic variability was observed between G. pallida populations distributed in the Europe and Ukraine, accounting for 82.3 per cent (P < 0.05) of the genetic variability inferred from the mitochondrial cytochrome b gene polymorphisms within the populations studied. G. pallida populations selected on three sources of resistance were similar but not identical indicat- ing that changes in mtDNA haploid type frequency had taken place as a result of the selection regime, but the marker used was not yet applicable for virulence monitoring. Conclusions. The obtained data prove the hypothesis that G. pallida populations in Ukraine are the result of the continuing spread of the species within the Europe and not the consequence of additional introduction from the South America.

scholarly journals Hypotheses from mitochondrial DNA: congruence and conflict between DNA sequences and morphology in Dolichopodinae systematics (Diptera:Dolichopodidae)

2010 ◽  
Vol 24 (1) ◽  
pp. 32 ◽  
Author(s):  
Marc Pollet ◽  
Christoph Germann ◽  
Samuel Tanner ◽  
Marco Valerio Bernasconi
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Molecular Analysis ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Species Group ◽  
Data Matrix ◽  
Cyt B ◽  
Molecular Phylogenetic ◽  
Species Groups

The molecular phylogeny of the subfamily Dolichopodinae (Diptera : Dolichopodidae) is reconstructed based on 79 species of 7 dolichopodine genera as ingroup, and 10 non-dolichopodine species from different genera as outgroup. A Bayesian analysis based on a mitochondrial DNA dataset consisting of 1702 characters (COI : 810; 12S : 366; 16S : 526) was carried out. Genital and non-genital morphological characters from a hitherto unpublished data matrix (based on 57 Dolichopodidae species) were used to explain and support the lineages hypothesised by our molecular phylogenetic analysis. The monophyly of the subfamily Dolichopodinae, and of the genera Dolichopus and Gymnopternus, was confirmed. The molecular analysis yielded nine species groups in Dolichopus that were proposed in previous studies using COI and Cyt-b. No evidence was found to support a clade including Dolichopus, Ethiromyia, and Gymnopternus. The genus Hercostomus proved polyphyletic with respect to Poecilobothrus, Sybistroma, and Gymnopternus. The following lineages were represented by strongly supported clades: Hercostomus germanus species group, H. vivax species group, H. nigrilamellatus species group, H. plagiatus species group, H. longiventris species group, H. fulvicaudis species group, and Poecilobothrus, Gymnopternus, Tachytrechus and Sybistroma (including Hercostomus nanus and H. parvilamellatus). Two clades that were previously established on the basis of morphology were confirmed in our phylogenetic analysis: (i) Poecilobothrus and the flower-feeding Hercostomus germanus species group, and (ii) the H. longiventris lineage and Sybistroma. In most cases, the groups identified in the molecular analysis could be supported and explained by morphological characters. Species of the Hercostomus germanus species group, Poecilobothrus, the Hercostomus longiventris species group, and a Sybistroma subclade have a similar microhabitat affinity.

scholarly journals Mitochondrial DNA Diversity of Terubok (Tenualosa toli) from Daro and Mukah, Sarawak Inferred by Partial Cytochrome b (Cyt-B)

2015 ◽  
Vol 10 (2) ◽  
pp. 92-101 ◽  
Author(s):  
Abdul Hadi Abdul Aziz ◽  
Zakirah Tarmizi ◽  
Nabilah Mohamad Ali ◽  
Nur Asma Ariffin ◽  
Muhd Danish Daniel Abdullah ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome B ◽  
Cyt B ◽  
Dna Diversity

Evaluation of the dark field method for large association of spread DNA

1978 ◽  
Vol 36 (2) ◽  
pp. 190-191
Author(s):  
Douglas C. Barker
Keyword(s):  
Electron Microscopy ◽  
Molecular Weight ◽  
Mitochondrial Dna ◽  
Extraction Method ◽  
Field Method ◽  
Dark Field ◽  
Kinetoplast Dna ◽  
Field Electron ◽  
Field Electron Microscopy ◽  
Dark Field Electron

A number of satisfactory methods are available for the electron microscopy of nicleic acids. These methods concentrated on fragments of nuclear, viral and mitochondrial DNA less than 50 megadaltons, on denaturation and heteroduplex mapping (Davies et al 1971) or on the interaction between proteins and DNA (Brack and Delain 1975). Less attention has been paid to the experimental criteria necessary for spreading and visualisation by dark field electron microscopy of large intact issociations of DNA. This communication will report on those criteria in relation to the ultrastructure of the (approx. 1 x 10-14g) DNA component of the kinetoplast from Trypanosomes. An extraction method has been developed to eliminate native endonucleases and nuclear contamination and to isolate the kinetoplast DNA (KDNA) as a compact network of high molecular weight. In collaboration with Dr. Ch. Brack (Basel [nstitute of Immunology), we studied the conditions necessary to prepare this KDNA Tor dark field electron microscopy using the microdrop spreading technique.

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