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

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.

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Genetic Variation Study within (Ompok bimaculatus and Clupisoma sinensis) Populations in Samarra Dam Middle of Iraq and Shatt Al-Arab Southern of Iraq belonging to Tigris River Using Mitochondrial Cytochrome b Gene

Genetics of Aquatic Organisms ◽

10.4194/2459-1831-v3_2_03 ◽

2019 ◽

Vol 3 (2) ◽

Author(s):

Rabeeha Mankhi Jebur

Keyword(s):

Genetic Variation ◽

Cytochrome B ◽

Cytochrome B Gene ◽

Mitochondrial Cytochrome ◽

Tigris River ◽

Mitochondrial Cytochrome B ◽

Mitochondrial Cytochrome B Gene ◽

Ompok Bimaculatus

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

Journal of Biodiversity Conservation and Bioresource Management ◽

10.3329/jbcbm.v5i1.42182 ◽

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

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

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d200103 ◽

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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Genetic Variation Analysis between Wild and Cultured Pangasianodon hypopthalmus Using COI and Cytochrome b Among Asian Countries

Science Letters ◽

10.24191/sl.v16i1.15422 ◽

2022 ◽

Vol 16 (1) ◽

pp. 84

Author(s):

Nik Azwarina R Azmi ◽

Lyena Watty Zuraine Ahmad ◽

Roziah Kambol ◽

Sharifah Aminah Syed Mohamad ◽

Farizan Aris ◽

...

Keyword(s):

Genetic Variation ◽

Cytochrome B ◽

Phylogenetic Trees ◽

Cytochrome B Gene ◽

Asian Countries ◽

Base Pairs ◽

Partial Region ◽

Pangasianodon Hypophthalmus ◽

Wide Range ◽

Striped Catfish

One of the top species in the aquaculture sector, known as striped catfish or Pangasianodon hypophthalmus, is an important and valuable freshwater fish in many countries. Due to the high demand for this species, their number has declined to "threatened" levels. Hence, the purpose of this study is to analyse the genetic variation of wild and cultured striped catfish collected from five producers in Asian countries; Thailand, Vietnam, Indonesia, India, and Philippines, by using mitochondrial DNA partial region data sequence; CO1 and cytochrome b gene. Population analyses using 395 base pairs length for CO1 and 275 base pairs length of cytochrome b partial region nucleotide sequence have shown no significance difference between wild and cultured striped catfish. Vietnam species had shown a wide range of genetic distance of the intrapopulation compared with other countries in the range of 0.000-0.040 for CO1 gene and 0.003-0.008 for cytochrome b gene. The Neighbour-joining method has also been used to construct phylogenetic trees using CO1 gene; the tree formed few subclades with mixed populations, and the tree using cytochrome b showed only Vietnam species divided into a few sub-populations. For the other four countries, Thailand, Indonesia, India, and Philippines were in the same group. Hence, this study's findings may provide a reference for inter and intra-relationships of P. hypophthalmus that may help in the aquaculture activity of this striped catfish.

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Genetic Variation of Eight Indonesian Swamp-Buffalo Populations Based on Cytochrome b Gene Marker

Tropical Animal Science Journal ◽

10.5398/tasj.2020.43.1.1 ◽

2020 ◽

Vol 43 (1) ◽

pp. 1-10

Author(s):

M. Rusdin ◽

D. D. Solihin ◽

A. Gunawan ◽

C. Talib ◽

C. Sumantri

Keyword(s):

Genetic Variation ◽

Cytochrome B ◽

Cytochrome B Gene ◽

Gene Marker ◽

Swamp Buffalo

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Genetic Variation in Cytochrome b-Hinf1 and -Alu1 Gene Correlated to Body Size in Soang Gourami (Osphronemus goramy Lacepede, 1801) from Single Spawning

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v9i2.9301 ◽

2017 ◽

Vol 9 (2) ◽

Author(s):

Agus Nuryanto ◽

Nael Huda Qonita ◽

Hendro Pramono ◽

Kusbiyanto Kusbiyanto ◽

Petrus Hary Tjahja Soedibja

Keyword(s):

Genetic Variation ◽

Body Size ◽

Cytochrome B ◽

Restriction Enzymes ◽

Cytochrome B Gene ◽

Rflp Marker ◽

Rflp Markers ◽

Molecular Technique ◽

Pcr Rflp ◽

Body Sizes

Soang gourami fingerling shows variable body sizes eventhough resulted from single spawning. Differences in body sizes among individuals is assumed to be correlated to their genetic component which can be studied using cytochrome b gene PCR-RFLP marker. This study aimed to determine specific PCR-RFLP marker among different sizes of soang gourami collected from single spawning. Genomic DNA was isolated using Chelex method. Cytochrome b gene were amplified and digested using four restriction enzymes. Specific markers were analyzed descriptivelly based on DNA band pattern appear in agarose gel. Ther result showed that PCR-RFLP markers of Cytochrome b-HinfI of 315bp, and 210bp, and also Cytochrome b-AluI of 334bp and 189bp are specific markers for large individuals, whereas small individuals are characterized by having Cytochrome b- HinfI 366bp, and 159bp and Cytochrome b-AluI 525bp fragments. It is observed that genetic variation of Cytochrome b-HinfI and -AluI markers are possitively correlated to body size in soang gourami fingerling. Therefore, both cytochrome b-HinfI and -AluI gene can be reffered as specific markers to differentiate among different sizes of soang gourami strain fingerling from single spawning. This result proved that genetic divergences among individuals can be related with certain quantitative characters, such size related. Therefore our study can contribute on fisheries development, especially by providing new technique for fingerling selection to obtain high quality fingerling and also provide new insight the application of molecular technique in fisheries.

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

Jurnal Iktiologi Indonesia ◽

10.32491/jii.v21i1.552 ◽

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.

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