DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus
Objectives: DNA barcoding technique for fish identification is an effective, rapid, and precise method as compared to the morphological method. Cytochrome c oxidase subunit 1 gene-based DNA barcoding is frequently used in species identification and biodiversity studies. The current study was designe...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-08-01
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| Series: | Journal of King Saud University: Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1018364723001878 |
| _version_ | 1797774811710095360 |
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| author | Aiman Sajjad Farhat Jabeen Muhammad Ali Saba Zafar |
| author_facet | Aiman Sajjad Farhat Jabeen Muhammad Ali Saba Zafar |
| author_sort | Aiman Sajjad |
| collection | DOAJ |
| description | Objectives: DNA barcoding technique for fish identification is an effective, rapid, and precise method as compared to the morphological method. Cytochrome c oxidase subunit 1 gene-based DNA barcoding is frequently used in species identification and biodiversity studies. The current study was designed to identify the fishes with the help of DNA barcoding method resulting COI gene sequences, which were used in the construction of genetic diversity and evolutionary history of Wallago attu inhabiting different sites of the River Indus. Methods: The short mDNA gene sequence of 650 base pairs (COI) was amplified, sequenced, and analyzed by using different bioinformatics tools. The Pairwise distance and phylogenetic analysis by Maximum Likelihood (ML) tree based on Kimura 2 Parameter method was constructed by using MEGA 11 software. Results: Pairwise genetic distance among species showed less divergence between a minimum of 0.000% and a maximum of 0.038%. The Percentage base composition of sequenced samples was calculated and overall AT content (53.7%) was found higher in all sequences as compared to GC content (46.2%). The Phylogenetic tree revealed that species clustered differently under diverse nodes. It revealed that fish species clustered together because they were in the same order and family. QR code in this study was first time developed to guide misleading and fraud cases. Conclusions: These results showed that fish species share identical genera but with diverse genetic variations due to diverse habitats involving a common ancestor. The COI barcodes generated in the current study will help in species identification. |
| first_indexed | 2024-03-12T22:26:38Z |
| format | Article |
| id | doaj.art-610af1cb31954873bb5a887b99b51b96 |
| institution | Directory Open Access Journal |
| issn | 1018-3647 |
| language | English |
| last_indexed | 2024-03-12T22:26:38Z |
| publishDate | 2023-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of King Saud University: Science |
| spelling | doaj.art-610af1cb31954873bb5a887b99b51b962023-07-22T04:51:26ZengElsevierJournal of King Saud University: Science1018-36472023-08-01356102725DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River IndusAiman Sajjad0Farhat Jabeen1Muhammad Ali2Saba Zafar3Government College University Faisalabad, PakistanGovernment College University Faisalabad, Pakistan; Corresponding author.Bahauddin Zakariya University, Multan, PakistanGovernment College University Faisalabad, PakistanObjectives: DNA barcoding technique for fish identification is an effective, rapid, and precise method as compared to the morphological method. Cytochrome c oxidase subunit 1 gene-based DNA barcoding is frequently used in species identification and biodiversity studies. The current study was designed to identify the fishes with the help of DNA barcoding method resulting COI gene sequences, which were used in the construction of genetic diversity and evolutionary history of Wallago attu inhabiting different sites of the River Indus. Methods: The short mDNA gene sequence of 650 base pairs (COI) was amplified, sequenced, and analyzed by using different bioinformatics tools. The Pairwise distance and phylogenetic analysis by Maximum Likelihood (ML) tree based on Kimura 2 Parameter method was constructed by using MEGA 11 software. Results: Pairwise genetic distance among species showed less divergence between a minimum of 0.000% and a maximum of 0.038%. The Percentage base composition of sequenced samples was calculated and overall AT content (53.7%) was found higher in all sequences as compared to GC content (46.2%). The Phylogenetic tree revealed that species clustered differently under diverse nodes. It revealed that fish species clustered together because they were in the same order and family. QR code in this study was first time developed to guide misleading and fraud cases. Conclusions: These results showed that fish species share identical genera but with diverse genetic variations due to diverse habitats involving a common ancestor. The COI barcodes generated in the current study will help in species identification.http://www.sciencedirect.com/science/article/pii/S1018364723001878Wallago attuMorphological IdentificationCOI geneDNA barcodingPhylogenetic analysis |
| spellingShingle | Aiman Sajjad Farhat Jabeen Muhammad Ali Saba Zafar DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus Journal of King Saud University: Science Wallago attu Morphological Identification COI gene DNA barcoding Phylogenetic analysis |
| title | DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus |
| title_full | DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus |
| title_fullStr | DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus |
| title_full_unstemmed | DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus |
| title_short | DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus |
| title_sort | dna barcoding and phylogenetics of wallago attu using mitochondrial coi gene from the river indus |
| topic | Wallago attu Morphological Identification COI gene DNA barcoding Phylogenetic analysis |
| url | http://www.sciencedirect.com/science/article/pii/S1018364723001878 |
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