Genetic diversity of the cytochrome b gene fragment haplotypes in red-backed vole Myodes (Clethrionomys) rutilus Pallas, 1779

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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Molecular identification of cephalopod species by FINS and PCR-RFLP of a cytochrome b gene fragment

European Food Research and Technology ◽

10.1007/s00217-003-0788-y ◽

2003 ◽

Vol 217 (6) ◽

pp. 524-529 ◽

Cited By ~ 26

Author(s):

Mar�a Jos� Chapela ◽

Carmen G. Sotelo ◽

Ricardo I. P�rez-Mart�n

Keyword(s):

Cytochrome B ◽

Molecular Identification ◽

Cytochrome B Gene ◽

Gene Fragment ◽

Cephalopod Species ◽

Pcr Rflp

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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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