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Updated: Jun 4, 2025
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Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
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In silico analysis of mitochondrial DNA genes: implication for conservation of Tor putitora (Hamilton, 1822)
Kushal Thakur1, Deepika Sharma1, Ankita Sharma2
1Department of Animal Sciences, Central University of Himachal Pradesh, 176206, Dharamsala, India.
Scientific Reports
|January 2, 2025
Summary
Tor putitora, an endangered indicator fish, shows significant genetic variation. Analysis suggests population expansion, likely due to habitat destruction, highlighting the need for conservation efforts.
Area of Science:
- Ichthyology
- Conservation Genetics
- Molecular Ecology
Background:
- Tor putitora is an endangered cyprinid fish, vital for cold-water ecosystems and as an indicator of aquatic health.
- Understanding its genetic diversity is crucial for effective conservation and management strategies.
Purpose of the Study:
- To investigate the haplotypic diversity, genetic variation, and population structure of Tor putitora.
- To analyze genetic data using mitochondrial genes (COI and Cyt b) for conservation insights.
Main Methods:
- Bioinformatic analysis of 106 COI and 183 Cyt b gene sequences from GenBank.
- Utilized 2 reference genome sequences for comparative analysis.
- Calculated haplotype and nucleotide diversity, identified ancestral haplotypes, and performed neutrality tests (Tajima's D, Fu's Fs).
Main Results:
- Identified 18 COI and 85 Cyt b haplotypes, with mutations at numerous sites.
- COI gene showed moderate haplotype diversity (0.630) and low nucleotide diversity (0.00662).
- Cyt b gene exhibited higher haplotype diversity (0.804) and low nucleotide diversity (0.00582).
- Negative values in neutrality tests suggest population expansion potentially linked to habitat destruction.
Conclusions:
- Genetic variability within and among Tor putitora populations is essential for species conservation.
- Integrating genetic diversity data into conservation planning can improve breeding programs and habitat restoration.
- The findings underscore the impact of environmental changes on endangered fish populations.
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