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Complete mitochondrial genome sequence of Catla catla (Hamilton, 1822) from the Halda river of Bangladesh.

ABSTRACT: Catla (Catla catla) is one of the fastest-growing major carp found in South Asia as well as Bangladesh. Catla catla is the second most popular indigenous carp species in the freshwater aquaculture industry of Bangladesh due to its relatively good taste and high market price. In this study, we disclosed the complete mitochondrial genome sequence of Bangladeshi Catla fish from Halda river located in Chittagong. The circular mitogenome of Catla catla is 16,597 bp in length and nucleotide composition is AT-based (72%), contains 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a D-loop (control region).

SUBMITTER: Kibria MM

PROVIDER: S-EPMC7782268 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Complete mitochondrial genome sequence of Catla catla (Hamilton, 1822) from the Halda river of Bangladesh.

Kibria M M MM Islam N N Billah M M Shawrob K S M KSM Shawrob K S M KSM Rumi M H MH Siddiki Amam Zonaed AZ

Mitochondrial DNA. Part B, Resources 20200830 3

Catla (Catla catla) is one of the fastest-growing major carp found in South Asia as well as Bangladesh. Catla catla is the second most popular indigenous carp species in the freshwater aquaculture industry of Bangladesh due to its relatively good taste and high market price. In this study, we disclosed the complete mitochondrial genome sequence of Bangladeshi Catla fish from Halda river located in Chittagong. The circular mitogenome of Catla catla is 16,597 bp in length and ...[more]

PMID: 33458116

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Project description:Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2 bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with Fst values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics.

Dataset Information

Complete mitochondrial genome sequence of Catla catla (Hamilton, 1822) from the Halda river of Bangladesh.

Publications

Complete mitochondrial genome sequence of <i>Catla catla</i> (Hamilton, 1822) from the Halda river of Bangladesh.

Similar Datasets

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