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 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 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.

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.    

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 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 Morphometrics and genetic diversity of Tegal, Magelang and their crossbred ducks based on Cytochrome b gene

2018 ◽  
Vol 43 (1) ◽  
pp. 9
Author(s):  
H. Henrik ◽  
D. Purwantini ◽  
I. Ismoyowati
Keyword(s):  
Genetic Diversity ◽  
Body Weight ◽  
Genetic Distance ◽  
Cytochrome B ◽  
Body Length ◽  
The Body ◽  
Chest Circumference ◽  
Neck Length ◽  
Significant Difference ◽  
Cyt B Gene

This experiment was conducted to study the morphometric and genetic diversity of Tegal, Magelang, and their crossbred ducks. Each ten female about twenty weeks old ducks from Tegal, Magelang, Gallang, and Maggal ducks, respectively, were used as the group materialss. The body weight, chest circumference, body length, shank length, neck length, and pubis width were recorded and tested by analysis of variance of one way classification as the morphometric characteristics. Polymorphism of cytochrome b (cyt b) gene on mitochondrial DNA (mtDNA) was analyzed by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). Genetic distance was analyzed based on value of heterozygosity, whereas the phylogeny tree was reconstructed using MEGA6 software. The results showed there were highly significant difference (P<0.01) on body weight, chest circumference, body length, and neck length between population, while shank and pubis width were not significant different. The genetic distance between Gallang and Maggal ducks (0.206) was higher than Tegal and Magelang ducks (0.169). It is concluded that the reciprocal crosses increased the morphometric and genetic diversity of Indonesian local duck population.

scholarly journals KERAGAMAN GENETIK IKAN TIGER FISH (Datnioides sp.) ASAL KALIMANTAN DAN SUMATERA

2018 ◽  
Vol 13 (3) ◽  
pp. 191
Author(s):  
Melta Rini Fahmi ◽  
Erma Primanita Hayuningtyas ◽  
Mochammad Zamroni ◽  
Bastiar Nur ◽  
Shofihar Sinansari
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Cytochrome B ◽  
Molecular Identification ◽  
Coi Gene ◽  
Cyt B ◽  
Cytochrome Oxidase 1 ◽  
Rag2 Gene

Ikan tiger fish (Datnioides sp.) merupakan ikan hias air tawar yang memiliki nilai ekonomis penting. Distribusi populasi ikan ini meliputi Papua, Kalimantan, dan Sumatera, dengan tingkat eksploitasi yang cukup tinggi di dua lokasi terakhir. Penelitian ini dilakukan untuk mendapatkan informasi keragaman genetik ikan tiger fish yang mendiami perairan Kalimantan dan Sumatera. Sebanyak 24 sampel ikan uji dikoleksi dari Sungai Kapuas, Kalimantan Barat dan Sungai Musi, Sumatera Selatan. Penelitian dilakukan dalam dua tahap, tahap pertama yaitu identifikasi molekuler dengan menggunakan DNA barcoding gen cytochrome oxidase 1 (COI), tahap kedua adalah analisis keragaman genetik dengan menggunakan marka DNA mitokondria gen cytochrome b (Cyt b), dan DNA inti gen recombination activating gene (RAG2). Hasil identifikasi secara molekuler menunjukkan bahwa ikan hasil koleksi memiliki kesamaan genetik sebesar 100% dengan spesies D. undecimradiatus. Keragaman genetik ikan tiger fish antar populasi berkisar pada nilai 0,023 (standar deviasi 0,001) sedangkan keragaman intra populasi adalah sebesar 0,002 dan 0,003 masing-masing untuk populasi Kalimantan dan Sumatera. Jarak genetik sampel baik yang berasal dari Sumatera maupun Kalimantan dengan spesies D. undeciumradiatus masing-masing 0,003 dan 0,006; sedangkan dengan spesies D. microlepis yaitu 0,142. Analisis menggunakan gen RAG2 menunjukkan sampel yang diuji memiliki struktur populasi yang terpisah ditandai dengan terjadinya mutasi pada enam nukleotida dan tiga asam amino.The Tiger fish (Datnioides sp.) is a freshwater ornamental fish that has important economic value. The distribution of this fish included Papua, Kalimantan, and Sumatra, but intensive exploitation occurs in the last two population. This research was conducted to obtain the genetic diversity of tiger fish that inhabited in Kalimantan and Sumatra. A total of 24 fish were collected from Kapuas River, West Kalimantan and Musi River, at Sumatra. The study was conducted in two stages, the first stage is molecular identification of sample by using DNA barcoding cytochrome oxidase 1 (COI) gene, the second stage is analyses of genetic diversity of tiger fish within and between population by using the mitochondrial DNA cytochrome b (Cyt b) gene, and nucleus DNA recombination (RAG2) gene. The molecular identification has shown that the collected fish has a genetic similarity of 100% with D. undecimradiatus. The genetic diversity of tiger fish between populations is 0.023 (standard deviation of 0.001) whereas intra-population is 0.002 and 0.003 for Kalimantan and Sumatra, respectively. The genetic distance of samples with species D. undeciumradiatus were 0.003 and 0.006 for Kalimantan and Sumatera, respectively, whereas the genetic distance with D. microlepis was 0.142. The analysis of mutation on RAG2 gene shows there are six nucleotides and three amino acids have mutation.

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

Phylogenetic analysis based studies on genetic variation of Cytochrome b gene of Indian peafowl (Pavo cristatus) in Pakistan

2017 ◽  
Author(s):  
Junaid Naseer ◽  
Khalid Mahmood Anjum ◽  
Waseem Ahmad Khan ◽  
Muhammad Imran ◽  
Muhammad Ishaque ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Private Sector ◽  
Cytochrome B ◽  
Cytochrome B Gene ◽  
Universal Primers ◽  
Sample Collection ◽  
Government Sector ◽  
Pavo Cristatus ◽  
Cyt B Gene ◽  
Breeding Farms

This study was designed to analyze genetic variation between Indian peafowl available at different locations by targeting the Cytochrome b gene. A total of ten birds (n=10) were selected randomly for sample collection. Five birds were selected from Government sector and five from private breeding farms. DNA was extracted, purified and measured by using Nano drop. Extracted DNA was amplified using universal primers targeting Cytochrome b gene on polymerase chain reaction (PCR). PCR product was run on a gel for the desired DNA bands. DNA from gel was eluted and sent for sequencing. The sequences were compared with a reference reported sequence of cyt b gene of Indian peafowl with Accession No. L08379.1to find out the genetic diversity. Indian peafowl of government sector showed more similarity ³95% rather than bird of private sector with ³90% homology with reference Accession No. More genetic variation, which is the guarantee of resistance to disease and environmental fitness among the Indian peafowl at private sector, might be due to random reproductive behavior.

Revisions of two poorly known species of Opisthotropis Günther, 1872 (Squamata: Colubridae: Natricinae) with description of a new species from China

Zootaxa ◽  
2017 ◽  
Vol 4247 (4) ◽  
pp. 391 ◽  
Author(s):  
YING-YONG WANG ◽  
QIANG GUO ◽  
ZU-YAO LIU ◽  
ZHI-TONG LYU ◽  
JIAN WANG ◽  
...  
Keyword(s):  
Southern China ◽  
Phylogenetic Analyses ◽  
Eastern China ◽  
Morphological Characters ◽  
Species Boundaries ◽  
Integrative Approach ◽  
Cyt B ◽  
Molecular Phylogenetic ◽  
Cyt B Gene ◽  
A New Species

The previous descriptions of Opisthotropis maxwelli Boulenger, 1914 and O. andersonii (Boulenger, 1888) were considered imperfect due to the limited number of specimens. This may in turn cause a problem for accurate species identification. In our study, the species boundaries of these two species were investigated using an integrative approach incorporating morphological characters and molecular phylogenetic analyses of the mitochondrial Cyt b gene of 26 specimens of nine known Opisthotropis species collected from south-eastern China. Our results surprisingly revealed a new cryptic species, Opisthotropis shenzhenensis sp. nov., from Shenzhen and Dongguan, Guangdong Province, southern China. Further, we re-described O. maxwelli based on several specimens from Fujian and Guangdong, and O. andersonii based on a series of specimens from Hong Kong, Shenzhen and Guangzhou, China. We provide an updated identification key to all described Opisthotropis species from China. 

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