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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ftdoajarticles:oai:doaj.org/article:610af1cb31954873bb5a887b99b51b96 2023-07-02T03:31:43+02:00 DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus Aiman Sajjad Farhat Jabeen Muhammad Ali Saba Zafar 2023-08-01T00:00:00Z https://doi.org/10.1016/j.jksus.2023.102725 https://doaj.org/article/610af1cb31954873bb5a887b99b51b96 EN eng Elsevier http://www.sciencedirect.com/science/article/pii/S1018364723001878 https://doaj.org/toc/1018-3647 1018-3647 doi:10.1016/j.jksus.2023.102725 https://doaj.org/article/610af1cb31954873bb5a887b99b51b96 Journal of King Saud University: Science, Vol 35, Iss 6, Pp 102725- (2023) Wallago attu Morphological Identification COI gene DNA barcoding Phylogenetic analysis Science (General) Q1-390 article 2023 ftdoajarticles https://doi.org/10.1016/j.jksus.2023.102725 2023-06-11T00:32:55Z 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. Article in Journal/Newspaper Attu Directory of Open Access Journals: DOAJ Articles Journal of King Saud University - Science 35 6 102725 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Wallago attu Morphological Identification COI gene DNA barcoding Phylogenetic analysis Science (General) Q1-390 |
spellingShingle |
Wallago attu Morphological Identification COI gene DNA barcoding Phylogenetic analysis Science (General) Q1-390 Aiman Sajjad Farhat Jabeen Muhammad Ali Saba Zafar DNA barcoding and phylogenetics of Wallago attu using mitochondrial COI gene from the River Indus |
topic_facet |
Wallago attu Morphological Identification COI gene DNA barcoding Phylogenetic analysis Science (General) Q1-390 |
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. |
format |
Article in Journal/Newspaper |
author |
Aiman Sajjad Farhat Jabeen Muhammad Ali Saba Zafar |
author_facet |
Aiman Sajjad Farhat Jabeen Muhammad Ali Saba Zafar |
author_sort |
Aiman Sajjad |
title |
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_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_sort |
dna barcoding and phylogenetics of wallago attu using mitochondrial coi gene from the river indus |
publisher |
Elsevier |
publishDate |
2023 |
url |
https://doi.org/10.1016/j.jksus.2023.102725 https://doaj.org/article/610af1cb31954873bb5a887b99b51b96 |
genre |
Attu |
genre_facet |
Attu |
op_source |
Journal of King Saud University: Science, Vol 35, Iss 6, Pp 102725- (2023) |
op_relation |
http://www.sciencedirect.com/science/article/pii/S1018364723001878 https://doaj.org/toc/1018-3647 1018-3647 doi:10.1016/j.jksus.2023.102725 https://doaj.org/article/610af1cb31954873bb5a887b99b51b96 |
op_doi |
https://doi.org/10.1016/j.jksus.2023.102725 |
container_title |
Journal of King Saud University - Science |
container_volume |
35 |
container_issue |
6 |
container_start_page |
102725 |
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1770271115608850432 |