scholarly journals Substitution and Haplotype Diversity Analysis on The Partial Sequence of The Mitochondrial DNA Cyt b of Indonesian Swamp Buffalo (Bubalus bubalis)

2015 ◽  
Vol 3 (2) ◽  
pp. 59
Author(s):  
Akhmad Sukri ◽  
Mohamad Amin ◽  
Aris Winaya ◽  
Abdul Gofur
Keyword(s):  
Mitochondrial Dna ◽  
Gene Sequence ◽  
Genetic Relationships ◽  
Haplotype Diversity ◽  
Bubalus Bubalis ◽  
Cyt B ◽  
Substitution Pattern ◽  
Silent Substitution ◽  
Swamp Buffalo ◽  
Cyt B Gene

<p>This research aims to investigate the substitution pattern of nucleotide base and haplotype diversity of Indonesian swamp buffalo (<em>Bubalus bubalis)</em> based on the mitochondrial DNA cyt b partial gene sequence. 17 samples were chosen from 7 different regions with each uniquely represents Indonesian biogeography which comprise Aceh, Riau, Madiun, Blitar, Lombok, South Borneo and Tana Toraja. The result of cyt b gene sequence alignment showed the presence of transition and transversion substitutions and the absence of insertion and deletion. The amount of transitions was found to be higher than that of transversions and the amount of substitution in pyrimidine was also higher than that in purine. The highest amount of transitions happened in base TàC which is a silent substitution. The result of median joining network analysis showed that Indonesian haplotype<em> Bubalus bubalis</em> could be classified into 16 haplotypes which form different haplogroups unique to their geographical region. The result of median joining network<em> </em>analysis also indicated that the genetic relationships of swamp buffaloes (<em>Bubalus bubalis) </em>in Indonesia are highly influenced by their geographical locations.</p>

scholarly journals Status and origin of Egyptian local rabbits in comparison with Spanish common rabbits using mitochondrial DNA sequence analysis

2020 ◽  
Vol 28 (2) ◽  
pp. 93
Author(s):  
Ahmed Mostafa Emam ◽  
Sandra Afonso ◽  
Pedro González-Redondo ◽  
G.M.K. Mehaisen ◽  
A.A.A. Azoz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Haplotype Diversity ◽  
Wild Rabbit ◽  
Cyt B ◽  
The Status ◽  
European Rabbits ◽  
Cyt B Gene ◽  
Cluster 2 ◽  
Haplotype A

<p>Mitochondrial DNA (mtDNA) and cytochrome b (cyt b) gene sequences were used to determine the status of genetic diversity and phylogeny for 132 individuals from local rabbit breeds in Egypt and Spain. The Egyptian local rabbit breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). However, the Spanish local rabbit breed was Spanish common rabbit (SCR). Previous breeds were compared with European Wild Rabbit taken from Albacete, Spain (EWR). A total of 353 mutations, 290 polymorphic sites, 14 haplotypes, 0.06126 haplotype diversity and -1.900 (&lt;em&gt;P&lt;/em&gt;&lt;0.05) for Tajima’s D were defined in this study. Haplotype A mostly occurred in 83.3% of Egyptian rabbits and 11.7% of EWR, while haplotype B occurred in 63.8% of Spanish rabbits and 36.2% of  the EGS breed. A total of 47 domestic and wild &lt;em&gt;Oryctolagus cuniculus&lt;/em&gt; published sequences were used to investigate the origin and relation among the rabbit breeds tested in this study. The most common haplotype (A) was combined with 44.7% of published sequences. However, haplotype B was combined with 8.5%. Haplotypes of Egyptian, SCR and EWR were scattered in cluster 1, while we found only one EGS haplotype with two haplotypes of EWR in cluster 2. Our results assumed that genetic diversity for ERB, EBB and SCR was very low. Egyptian breeds and SCR were introduced from European rabbits. We found that ERB and EBB belong to one breed.</p>

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.

Haplotype diversity in the mtDNA cyt b gene in round goby (Neogobius melanostomus (Pallas)) from the northwestern part of the Black Sea basin

2014 ◽  
Vol 50 (3) ◽  
pp. 274-279 ◽  
Author(s):  
Yu. V. Slynko ◽  
V. V. Stolbunova ◽  
S. V. Chebotar ◽  
V. V. Zamorov ◽  
A. N. Gurovskiy
Keyword(s):  
Black Sea ◽  
Round Goby ◽  
Haplotype Diversity ◽  
Neogobius Melanostomus ◽  
The Black Sea ◽  
Northwestern Part ◽  
Cyt B ◽  
Cyt B Gene

scholarly journals Population diversity of striped snakehead, Channa striata (Bloch, 1793) from Bekasi, West Java and Barito Kuala, South Kalimantan using Cytochrome B gene

2021 ◽  
Vol 21 (1) ◽  
pp. 61-73
Author(s):  
Gita Kusuma Rahayu ◽  
Dedy Duryadi Solihin ◽  
Nurlisa A Butet
Keyword(s):  
Genetic Distance ◽  
Cytochrome B ◽  
Southern China ◽  
Genetic Relationships ◽  
Population Diversity ◽  
Cytochrome B Gene ◽  
Cyt B ◽  
Channa Striata ◽  
Commercially Important ◽  
Cyt B Gene

Channa striata or striped snakehead is one of species from family Channidae that widely distributed from India, Southern China to Southeast Asia including Indonesia. It is a commercially important freshwater fish because of its taste and health benefits. High demand of this species trigger many efforts to increase its production, one of them is genetic monitoring. This study used complete Cytochrome b gene sequence of mtDNA for determining genetic variation in wild population of C. striata. C. striata samples (n=31) from two different locations in Indonesia were amplified and analyzed using MEGA ver 7.0. Sequences of 1140 bp complete cyt b gene revealed the presence of 2 haplotypes with 1137 bp conserved sites and 3 bp variable sites (0,26%). Overlapping haplotype was observed in samples from Bekasi, however there were only one haplotype in samples from South Borneo. Interspecies genetic were analysed with species from Genebank and showed that C. striata from Indonesia has close genetic relationships with C. striata from Borneo-Indonesia (MN057164.1) with genetic distance 0%. This study also revealed that C. striata from Indonesia were phylogenetically distinct with C. striata from China with 9,2%K2P genetic distance. Complete cyt b gene has been proven for assessing phylogenetic relationships and population diversity of C. striata in Indonesia.

scholarly journals DNA barcoding application of garfish (Hemirhampus sp.) in North Maluku Sea

2019 ◽  
Vol 19 (3) ◽  
pp. 463
Author(s):  
M. Janib Achmad ◽  
Martini Djamhur ◽  
M. Abjan Fabanyo ◽  
Nebuchadnezzar Akbar
Keyword(s):  
Polymerase Chain Reaction ◽  
Gene Sequence ◽  
Dna Amplification ◽  
Genetic Distances ◽  
Cyt B ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Cyt B Gene ◽  
Alignment Analysis ◽  
Dna Bar Coding

The purpose of this study was to identify the species of garfish in the waters of north Maluku by applying DNA bar-coding techniques. The method used in the study was the primary design of DNA extraction and isolation, and DNA amplification through polymerase chain reaction. The results showed that Gen Cyt b analysis amplified ± 350 bp amplicon and for the alignment analysis showed that the amplification sample sequence had similarity with the Cyt b gene sequence of Hemiramphus balao with value of 97%. Sequence analysis showed that the six specimens had very low genetic distances. It can be concluded that the isolate samples of garfish have a very close kinship.

Cytochrome b (Cyt-b) gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae), with phylogenetic and taxonomic insights

2007 ◽  
Vol 152 (4) ◽  
pp. 757-773 ◽  
Author(s):  
Y. P. Kartavtsev ◽  
T.-J. Park ◽  
K. A. Vinnikov ◽  
V. N. Ivankov ◽  
S. N. Sharina ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Cytochrome B ◽  
Gene Sequence ◽  
Cyt B ◽  
Flatfish Species ◽  
Gene Sequence Analysis ◽  
Cyt B Gene

scholarly journals Microsatellite and mitochondrial DNA analyses unveil the genetic structure of native sheep breeds from three major agro-ecological regions of India

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rekha Sharma ◽  
Sonika Ahlawat ◽  
Himani Sharma ◽  
Priyanka Sharma ◽  
Poonam Panchal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Relationships ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Population Expansion ◽  
Scientific Management ◽  
Ecological Zones ◽  
Sheep Breeds ◽  
Indigenous Sheep

AbstractSheep farming has been fundamental to many civilizations in the world and is practiced in India since antiquity. Several thousand years of adaptation to local environmental conditions and selective breeding have evolved 44 sheep breeds in India. They are paramount in terms of economic, scientific, and cultural heritage. Genetic characterization information is imperative for sustainable utilization and conservation of ovine heritage. In this study, the genetic diversity, differentiation, and structure of 11 indigenous sheep breeds from three different agro-ecological zones of India were explored with genomic microsatellite loci and mitochondrial DNA (D loop). The estimated diversity parameters indicated that populations retained high levels of genetic diversity (Na = 8.27 ± 0.17; Ho = 0.65 ± 0.01), which provides an optimistic viewpoint for their survival. However, significant inbreeding was also observed in the nine populations. Moderate genetic differentiation existed among the groups (FST = 0.129 ± 0.012), and most likely clusters existing in the dataset are seven. Phylogenetic clustering was in line with the geographical locations of sheep populations. Mitochondrial sequences revealed high haplotype diversity with the existence of maternal haplogroups A, B, and C, and signals of population expansion. Decreased genetic diversity and unique maternal lineage (C) in endangered Tibetan and Bonpala sheep breed, warrant their immediate scientific management. Overall, the quantitative data reported here on the extant variability, and genetic relationships among the Indian sheep breeds, provide critically important inputs that will be valuable for the decision-making process on their management, both for the conservation of endangered breeds, and formulation of breeding programs to check genetic erosion.

On the Gene Pool of Roe Deer (Capreolus) of Eastern Europe: Analysis of the Cyt b Gene Sequence Variability

2018 ◽  
Vol 54 (7) ◽  
pp. 825-831
Author(s):  
N. V. Kashinina ◽  
A. A. Danilkin ◽  
E. Y. Zvychaynaya ◽  
M. V. Kholodova ◽  
V. M. Kiryakulov
Keyword(s):  
Eastern Europe ◽  
Gene Pool ◽  
Gene Sequence ◽  
Roe Deer ◽  
Cyt B ◽  
Sequence Variability ◽  
Cyt B Gene

scholarly journals VARIASI INTERSPESIFIK JULANG (AVES: BUCEROTIDAE) INDONESIA BERDASARKAN GEN CYTOCHROME-B DNA MITOKONDRIA

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Jarulis Jarulis ◽  
Dedy Duryadi Solihin ◽  
Ani Mardiastuti ◽  
Lilik Budi Prasetyo
Keyword(s):  
Genetic Distance ◽  
Cytochrome B ◽  
Genetic Information ◽  
Gene Sequence ◽  
Conservation Management ◽  
Cyt B ◽  
Spin Column ◽  
Outgroup Species ◽  
Variation Distance ◽  
Cyt B Gene

Genetic information of Indonesian hornbills (Julang) is still limited. We sequenced the cytochrome b gene of three hornbill species (Rhyticeros undulatus, R. plicatus, and Aceros cassidix) to explore their genetic variation, distance, and phylogenetic. Nine blood samples for Cyt b from three hornbill species were isolated with Dneasy® Blood and Tissue Kit base on Spin-Column Protocol, Qiagen. SNP, genetic distance, and phylogeny were calculated by MEGA 6.0 software. This study was found variations in the Cyt b gene sequence (849 bp) between three species Indonesian Julang. Rhyticeros undulatus had the most SNP compared to R. plicatus and Aceros cassidix. Substitution of synonyms is more common than substitution of synonyms and transition substitution frequency tends to be much higher than transversion substitution. The three species of Indonesian Julang were markedly separate with an average genetic distance of 5.25%. and separated with the outgroup species at a genetic distance of 9.43%. Cytochrome b sequence genes from these three hornbill species are novel for identifying and classifying hornbills, and could be applied to prevent illegal poaching and conservation management in Indonesia.    

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