scholarly journals Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene

2020 ◽  
Vol 13 (1) ◽  
pp. 96-103
Author(s):  
Dorothea Vera Megarani ◽  
Herjuno Ari Nugroho ◽  
Zahrah Prawita Andarini ◽  
Yura Dwi Risa B. R. Surbakti ◽  
Rini Widayanti
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Cytochrome B ◽  
Genetic Characterization ◽  
Phylogenetic Study ◽  
Cyt B ◽  
Phylogenetic Structure ◽  
Mitochondrial Cytochrome B ◽  
Sperata Seenghala ◽  
Cyt B Gene

Aim: This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences. Materials and Methods: The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software. Results: Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids). Conclusion: Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).

scholarly journals Mitochondrial genetics of Chlamydomonas reinhardtii: resistance mutations marking the cytochrome b gene.

Genetics ◽  
1991 ◽  
Vol 127 (2) ◽  
pp. 335-343 ◽  
Author(s):  
P Bennoun ◽  
M Delosme ◽  
U Kück
Keyword(s):  
Amino Acid ◽  
Chlamydomonas Reinhardtii ◽  
Cytochrome B ◽  
Mating Type ◽  
Sequence Similarity ◽  
Uniparental Inheritance ◽  
Cyt B ◽  
Wild Type ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Abstract We describe the genetic and molecular analysis of the first non-Mendelian mutants of Chlamydomonas reinhardtii resistant to myxothiazol, an inhibitor of the respiratory cytochrome bc1 complex. Using a set of seven oligonucleotide probes, restriction fragments containing the mitochondrial cytochrome b (cyt b) gene from C. reinhardtii were isolated from a mitochondrial DNA library. This gene is located adjacent to the gene for subunit 4 of the mitochondrial NADH-dehydrogenase (ND4), near one end of the 15.8-kb linear mitochondrial genome of C. reinhardtii. The algal cytochrome b apoprotein contains 381 amino-acid residues and exhibits a sequence similarity of about 59% with other plant cytochrome b proteins. The cyt b gene from four myxothiazol resistant mutants of C. reinhardtii was amplified for DNA sequence analysis. In comparison to the wild-type strain, all mutants contain an identical point mutation in the cyt b gene, leading to a change of a phenylalanine codon to a leucine codon at amino acid position 129 of the cytochrome b protein. Segregation analysis in tetrads from reciprocal crosses of mutants with wild type shows a strict uniparental inheritance of this mutation from the mating type minus parent (UP-). However, mitochondrial markers from both parents are recovered in vegetative diploids in variable proportions from one experiment to the next for a given cross. On the average, a strong bias is seen for markers inherited from the mating type minus parent.

scholarly journals Amino acid diversity on the basis of cytochrome b gene in Kacang and Ettawa Grade goats

2017 ◽  
Vol 42 (3) ◽  
pp. 135 ◽  
Author(s):  
D. A. Lestari ◽  
S. Sutopo ◽  
E. Kurnianto
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Marker ◽  
Cytochrome B ◽  
Genomic Dna ◽  
Cyt B ◽  
Specific Amino Acid ◽  
Pcr Method ◽  
Cyt B Gene ◽  
Amino Acid Diversity

The objectives of study were to identify and assess the amino acid diversity of Cytochrome b (Cyt b) gene, genetic marker and characteristic of specific amino acid in Kacang and Ettawa Grade goat. Nineteen heads of Kacang goat (KG) and twelve heads of Ettawa Grade goat (EG) were purposively sampled. The genomic DNA was isolated by Genomic DNA Mini Kit (Geneaid) and amplified Cyt b using PCR method with CytbCapF and CytbCapR primers and was sequenced. The results showed that there were two specific amino acids that distinguish KG and EG goat with C. hircus and C. aegagrus and four specific amino acids that distinguish KG and EG goat with C. falconeri, but there were no specific amino acids can be used as a genetic marker to distinguish between Kacang and EG goat. In conclusion, specific amino acids in Cyt b gene can be used as a genetic marker among KG and EG goat with 3 goat others comparator.

scholarly journals Kajian Penanda Genetik Gen Sitokrom b DNA Mitokondria Ikan Lais dari Sungai Kampar Riau

2018 ◽  
Vol 10 (1) ◽  
pp. 6
Author(s):  
Roza Elvyra ◽  
Dedy Duryadi Solihin
Keyword(s):  
Species Diversity ◽  
Molecular Marker ◽  
Phylogenetic Relationship ◽  
Cytochrome B ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Phylogenetic Marker ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

The mitochondrial cytochrome b (cyt-b) gene as a phylogenetic marker of lais fish Kryptopterus schilbeides from Kampar River in Riau has been studied. This is a prelimininary research on the utility of cyt-b gene as a molecular marker to obtain species diversity and phylogenetic relationship among Kryptopterus fishes from Kampar River. The primers of L14841 and H15149 were used to amplify the cyt-b gene. The results showed that K. schilbeides has isoleusine at site-81 and metionine at site-114; K. schilbeides from Kampar River and K. schilbeides from GenBank form a phylogeny cluster at 45% value.

scholarly journals Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh

2019 ◽  
Vol 5 (1) ◽  
pp. 25-30
Author(s):  
RA Begum ◽  
MT Alam ◽  
H Jahan ◽  
MS Alam
Keyword(s):  
Genetic Diversity ◽  
Cytochrome B ◽  
Tissue Sample ◽  
Sequence Similarity ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Multiple Sequence ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30

scholarly journals Molecular detection of cattle and buffalo species meat origin using mitochondrial cytochrome b (Cyt b) gene

2016 ◽  
Vol 2 (2) ◽  
pp. 177-182
Author(s):  
Sirazum Munira ◽  
Fatema Tuz Jahura ◽  
Md Munir Hossain ◽  
Mohammad Shamsul Alam Bhuiyan
Keyword(s):  
Cytochrome B ◽  
Genomic Dna ◽  
Molecular Technique ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Dna Yield ◽  
Mitochondrial Cytochrome B ◽  
Meat Samples ◽  
Species Specific ◽  
Cyt B Gene

The study was conducted to adopt PCR based technique for identification of species origin from meat samples of cattle and buffalo using mitochondrial cytochrome b (Cyt b) gene fragment. A total of 42 ear tissue and meat samples were collected from different slaughterhouses and farms of Mymensingh, Bogra and Rangpur districts and stored in 96% ethanol at room temperature. Genomic DNA was extracted from all samples using GeNet Bio genomic DNA isolation kit. The average DNA yield of considered samples was found 204.57 ng/?l where the purity ranged from 1.82–1.99. Two (2) pair species-specific primers were used to amplify Cyt b gene fragments of 472 bp and 124 bp for cattle and buffalo, respectively. The PCR results revealed different species specific amplified fragments which could discriminate between cattle (472 bp) and buffalo (124 bp) species precisely from pure and mixed samples of those species. This study suggests an accurate molecular technique for identification of cattle and buffalo species meat origin and differentiates species present in adulterated meat samples. In conclusion, this DNA based technique could be utilized for prevention of malpractice in slaughterhouse and chain shops and thereby to protect consumer’s right.Asian J. Med. Biol. Res. June 2016, 2(2): 177-182

scholarly journals Molecular detection of goat and sheep meat origin using mitochondrial cytochrome b gene

2016 ◽  
Vol 45 (2) ◽  
pp. 41-45
Author(s):  
FT Jahura ◽  
S Munira ◽  
AKFH Bhuiyan ◽  
MR Hoque ◽  
MSA Bhuiyan
Keyword(s):  
Cytochrome B ◽  
Molecular Technique ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Mitochondrial Cytochrome B ◽  
Indigenous Goat ◽  
Meat Species ◽  
Meat Samples ◽  
Species Specific ◽  
Cyt B Gene

The present study was conducted to discriminate between sheep and goat species meat origin utilizing mitochondrial cytochrome b (Cyt b) gene fragment. A total of 46 ear tissue and meat samples were collected from different slaughterhouses and farms of Mymensingh and Rangpur districts. Genomic DNA was extracted using GeNet Bio DNA isolation kit and DNA concentration and purity was quantified by NanoDrop spectrophotometer. Two pairs species specific primer were used to amplify Cyt b gene fragments. Selected primers were highly conserved across the breed within a species and worked well with the species of indigenous goat and sheep resulting similar size of the amplicons 330 and 585 bp respectively. The duplex PCR condition would enable to detect adulteration from goat and sheep mixed samples which revealed by two precise bands (330 and 585 bp) in a single reaction. This study suggests an accurate molecular technique for identification of sheep and goat meat species origin and differentiates species present in adulterate meat samples. In conclusion, this DNA based marker could be used for prevention of fraudulent practice in slaughterhouse and chain shops in Bangladesh.Bang. J. Anim. Sci. 2016. 45 (2): 41-45

Phylogeny of Old and New World Vultures (Aves: Accipitridae and Cathartidae) Inferred from Nucleotide Sequences of the Mitochondrial Cytochrome b Gene

1995 ◽  
Vol 50 (11-12) ◽  
pp. 868-882 ◽  
Author(s):  
Michael Wink
Keyword(s):  
Cytochrome B ◽  
New World ◽  
Genetic Relatedness ◽  
Nucleotide Sequences ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Old World ◽  
Mitochondrial Cytochrome B ◽  
Close Relationship ◽  
Cyt B Gene

Abstract The molecular phylogeny of 11 Old World and 5 New World vultures was inferred from nucleotide sequences of the mitochondrial cytochrome b (cyt b) gene. According to this analysis carrion-feeding has evolved independently at least three times during evolution: 1.) In the New World vultures, which are clearly separated from vultures of the family Accipitridae; 2.) in the Neophron-Gypaetus clade which is positioned at the base of the Accipitrid tree and 3.) in the Gyps-Aegypius-complex which encloses the largest group of Old World vultures. Thus the genetic data clearly show that the carrion-feeding lifestyles and associated morphologies shared by New and Old World vultures are rather based on convergence than on close genetic relatedness. Employing the cyt b sequences of 12 other members of the Falconiformes and 10 members of the Ciconiiformes (sensu Sibley and Monroe, 1990) the phylogenetic relationship between the three clades of vultures and these other taxa was assessed. New World Vultures appear to share distant ancestry with storks but a close relationship is unlikely.

scholarly journals Biochemical and Genetic Characterization of Mundticin KS, an Antilisterial Peptide Produced by Enterococcus mundtii NFRI 7393

2002 ◽  
Vol 68 (8) ◽  
pp. 3830-3840 ◽  
Author(s):  
Shinichi Kawamoto ◽  
Jun Shima ◽  
Rumi Sato ◽  
Tomoko Eguchi ◽  
Sadahiro Ohmomo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Characterization ◽  
Solid Phase ◽  
Exchange Chromatography ◽  
Nucleotide Sequencing ◽  
Lactobacillus Curvatus ◽  
Amino Acid Peptide ◽  
Enterococcus Mundtii

ABSTRACT Mundticin KS, a bacteriocin produced by Enterococcus mundtii NFRI 7393 isolated from grass silage in Thailand, is active against closely related lactic acid bacteria and the food-borne pathogen Listeria monocytogenes. In this study, biochemical and genetic characterization of mundticin KS was done. Mundticin KS was purified to homogeneity by ammonium sulfate precipitation, sequential ion-exchange chromatography, and solid-phase extraction. The gene cluster (mun locus) for mundticin KS production was cloned, and DNA sequencing revealed that the mun locus consists of three genes, designated munA, munB, and munC. The munA gene encodes a 58-amino-acid mundticin KS precursor, munB encodes a protein of 674 amino acids involved in translocation and processing of the bacteriocin, and munC encodes a mundticin KS immunity protein of 98 amino acids. Amino acid and nucleotide sequencing revealed the complete, unambiguous primary structure of mundticin KS; mundticin KS comprises a 43-amino-acid peptide with an amino acid sequence similar to that of mundticin ATO6 produced by E. mundtii ATO6. Mundticin KS and mundticin ATO6 are distinguished by the inversion of the last two amino acids at their respective C termini. These two mundticins were expressed in Escherichia coli as recombinant peptides and found to be different in activity against certain Lactobacillus strains, such as Lactobacillus plantarum and Lactobacillus curvatus. Mundticin KS was successfully expressed by transformation with the recombinant plasmid containing the mun locus in heterogeneous hosts such as E. faecium, L. curvatus, and Lactococcus lactis. Based on our results, the mun locus is located on a 50-kb plasmid, pML1, of E. mundtii NFRI 7393.

A molecular phylogenetic study of Hylopetes (Rodentia: Sciuridae) inferred from mitochondrial cytochrome-b gene

Biologia ◽  
2014 ◽  
Vol 69 (12) ◽  
Author(s):  
Farong Yu ◽  
Xiuzhen Lian ◽  
Zuoping Li ◽  
Mingren Xie
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Cytochrome B Gene ◽  
Phylogenetic Study ◽  
Molecular Phylogenetic Study ◽  
Mitochondrial Cytochrome B ◽  
Distinct Genus ◽  
Molecular Phylogenetic ◽  
Close Genetic Relationship ◽  
Tectonic Movements

AbstractTo elucidate the phylogenetic relationships of Hylopetes, the complete cytochrome-b gene sequences (1,140 bp) were determined from degraded museum specimens for phylogenetic study. The large genetic differences (18.1% to 20.7%) separate Eoglaucomys from Hylopetes as a distinct genus. Phylogenetic relationships reconstructed with maximum parsimony, maximum likelihood, and Bayesian methods show that all Hylopetes were genetically clustered as two major groups, the Indochinese Hylopetes group including H. alboniger and H. phayrei, and the Sundaic group consisting of H. lepidus, H. nigripes, and H. spadiceus. The close genetic relationship and the recent divergence suggest that the Indochinese group rapidly extended to their present distributions with the uplifting of the Himalayas last few million years ago, whereas the oceanic tectonic movements during the Pliocene-Pleistocene resulted in the current geographical distributions of the Sundaic group through alteration of dispersal across the islands of the Sunda Shelf.

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.

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