Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River Indus
Objectives: Genus Labeo of family Cyprinidae comprising of important group of fish species are known for ornamental purpose, food, extracting oil, medicinal value and for potential viable aquaculture. The present study was conducted to assess the morphometric and molecular identification of freshwat...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-04-01
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| Series: | Journal of King Saud University: Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1018364724000351 |
| _version_ | 1797262932055162880 |
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| author | Saba Zafar Farhat Jabeen Muhammad Ali Aiman Sajjad |
| author_facet | Saba Zafar Farhat Jabeen Muhammad Ali Aiman Sajjad |
| author_sort | Saba Zafar |
| collection | DOAJ |
| description | Objectives: Genus Labeo of family Cyprinidae comprising of important group of fish species are known for ornamental purpose, food, extracting oil, medicinal value and for potential viable aquaculture. The present study was conducted to assess the morphometric and molecular identification of freshwater fishes of genus Labeo including Catla catla, Labeo rohita, Labeo calbasu, Labeo gnius, Labeo bata from the three fish resources of River Indus, Punjab, Pakistan. Methods: Out of 75, thirty fish specimen were amplified and sequenced with 650 bp of mitochondrial COI gene for the evaluation of fish biodiversity, management and conservation by using different bioinformatics techniques. Results: Maximum and minimum genetic divergence between fishes of C. catla, L. calbasu, L. boga, L. gonius and L. rohita, were 0.052 to 0.105, respectively. Highest divergence was found between Labeo bata and Labeo rohita. Interspecific mean distance was found higher than intraspecific distance. In nucleotide base composition, AT contents was higher than GC contents indicated the clear pattern of anti-G bias. Transition rate was k1 = 8.84 for purines and transversional rate was k2 = 15.47 for pyrimidines with transition/transversion bias R = 5.62. Tajima D test and nucleotide diversity was measured D = 1.382883 and π = 0.049981 respectively. Positive value of D indicated a strong selective pressure and lack of population expansion. Thirty species were identified with e-value 0.0 and similar identity 99.85 %–100 % with maximum 600 bp length. Phylogenetic tree revealed two major clades with 95 % high bootstrap values identity showed closet relationship among these species. Conclusions: Current study supported the efficacy of the COI gene for the species identification in River Indus and develop the concept for establishing Pakistani fish gene bank which is still needed. |
| first_indexed | 2024-03-08T04:07:43Z |
| format | Article |
| id | doaj.art-8bf2fd1f969b421d847bd1f3c2361be3 |
| institution | Directory Open Access Journal |
| issn | 1018-3647 |
| language | English |
| last_indexed | 2024-04-25T00:04:58Z |
| publishDate | 2024-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of King Saud University: Science |
| spelling | doaj.art-8bf2fd1f969b421d847bd1f3c2361be32024-03-14T06:13:50ZengElsevierJournal of King Saud University: Science1018-36472024-04-01364103123Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River IndusSaba Zafar0Farhat Jabeen1Muhammad Ali2Aiman Sajjad3Department of Zoology, Government College University Faisalabad, PakistanDepartment of Zoology, Government College University Faisalabad, Pakistan; Corresponding author.Bahauddin Zakariya University, Multan, PakistanDepartment of Zoology, Government College University Faisalabad, PakistanObjectives: Genus Labeo of family Cyprinidae comprising of important group of fish species are known for ornamental purpose, food, extracting oil, medicinal value and for potential viable aquaculture. The present study was conducted to assess the morphometric and molecular identification of freshwater fishes of genus Labeo including Catla catla, Labeo rohita, Labeo calbasu, Labeo gnius, Labeo bata from the three fish resources of River Indus, Punjab, Pakistan. Methods: Out of 75, thirty fish specimen were amplified and sequenced with 650 bp of mitochondrial COI gene for the evaluation of fish biodiversity, management and conservation by using different bioinformatics techniques. Results: Maximum and minimum genetic divergence between fishes of C. catla, L. calbasu, L. boga, L. gonius and L. rohita, were 0.052 to 0.105, respectively. Highest divergence was found between Labeo bata and Labeo rohita. Interspecific mean distance was found higher than intraspecific distance. In nucleotide base composition, AT contents was higher than GC contents indicated the clear pattern of anti-G bias. Transition rate was k1 = 8.84 for purines and transversional rate was k2 = 15.47 for pyrimidines with transition/transversion bias R = 5.62. Tajima D test and nucleotide diversity was measured D = 1.382883 and π = 0.049981 respectively. Positive value of D indicated a strong selective pressure and lack of population expansion. Thirty species were identified with e-value 0.0 and similar identity 99.85 %–100 % with maximum 600 bp length. Phylogenetic tree revealed two major clades with 95 % high bootstrap values identity showed closet relationship among these species. Conclusions: Current study supported the efficacy of the COI gene for the species identification in River Indus and develop the concept for establishing Pakistani fish gene bank which is still needed.http://www.sciencedirect.com/science/article/pii/S1018364724000351Morphology and DNA barcodingFreshwater fish diversityPhylogenetic analysisFish conservationGenus Labeo |
| spellingShingle | Saba Zafar Farhat Jabeen Muhammad Ali Aiman Sajjad Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River Indus Journal of King Saud University: Science Morphology and DNA barcoding Freshwater fish diversity Phylogenetic analysis Fish conservation Genus Labeo |
| title | Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River Indus |
| title_full | Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River Indus |
| title_fullStr | Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River Indus |
| title_full_unstemmed | Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River Indus |
| title_short | Assessment of genetic diversity of freshwater genus Labeo through DNA barcoding and phylogenetic analysis inhabited in the River Indus |
| title_sort | assessment of genetic diversity of freshwater genus labeo through dna barcoding and phylogenetic analysis inhabited in the river indus |
| topic | Morphology and DNA barcoding Freshwater fish diversity Phylogenetic analysis Fish conservation Genus Labeo |
| url | http://www.sciencedirect.com/science/article/pii/S1018364724000351 |
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