Molecular characterization of small indigenous fish species (SIS) of Bangladesh through DNA barcodes

• Published in: Gene Vol. 684; pp. 53 - 57
• Main Authors: Ahmed, Md. Sagir, Chowdhury, Md. Miraj Kobad, Nahar, Luthfun
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 05-02-2019
• Subjects: Animals; Bangladesh; Barcoding; Base Composition - genetics; Base Sequence - genetics; Cytochrome c oxidase subunit I (COI); Databases, Genetic; DNA Barcoding, Taxonomic - methods; DNA, Mitochondrial; Electron Transport Complex IV - genetics; Fishes - classification; Fishes - genetics; Fresh Water; Genes, Mitochondrial - genetics; Genetic diversity; Genetic Speciation; Genetic Variation; Phylogeny; Small indigenous species (SIS); Bangladesh; DD; mtDNA; Cytochrome c oxidase subunit I (COI); Barcoding; NT; K2P; EN; Genetic diversity; CR; Bangladesh; DNA; LC; NUMTs; BOLD; COI; NJ; SIS; Small indigenous species (SIS); PCR; VU
• DOI: 10.1016/j.gene.2018.10.048
• EISSN: 1879-0038
• ISSN: 0378-1119

The mitochondrial DNA gene cytochrome oxidase subunit I (COI) has been adopted as a global bioidentification system for animals. This study represents the comprehensive molecular identification of small indigenous fish species (SIS) of Bangladesh assessed by DNA barcoding. DNA barcodes were generated from 81 SIS species belongs to the orders Clupeiformes, Cypriniforms, Siluriformes, Perciformes, Synbranchiformes, Beloniformes and Tetraodontiformes representing 55 genera and 24 families. For all the samples, %G were significantly lowered compared to other nucleotides and %GC compared to %AT. Also, a significantly lowered GC content was observed in second and third codon position compared to the first codon position in all samples. The average Kimura two-parameter (K2P) distances within genera, families, and orders were 15.83%, 19.14%, and 25.07%, respectively. The minimum and maximum K2P distance based genetic divergences were 0.19% and 57.14% respectively. Members of Cypriniformes, Siluriformes, and Perciformes were clustered separately in the neighbour-joining (NJ) tree. Nucleotide composition, GC distribution across codon positions, K2P distance, genetic divergence, and phylogenetic analyses reveal that these freshwater SIS fishes are genetically very diverse. Along with morphological data, we have confirmed the existence of seven new records of SIS fishes in Bangladesh using such barcode approach. These findings suggest that fishes can be discriminated using these barcode data without any confusion.
•We have barcoded 81 small indigenous species (SIS) fishes of Bangladesh.•Our barcode data can define the diversity of these SIS across genera, families, and orders.•We have confirmed the existence of seven new records of SIS fishes in Bangladesh