Abstract
Harpadon nehereus forms one of the most important commercial fisheries along the Bay of Bengal and the southeast coast of China. In this study, the genome-wide survey dataset first produced using next-generation sequencing (NGS) was used to provide general information on the genome size, heterozygosity and repeat sequence ratio of H. nehereus. About 68.74 GB of high-quality sequence data were obtained in total and the genome size was estimated to be 1315 Mb with the 17-mer frequency distribution. The sequence repeat ratio and heterozygosity were calculated to be 52.49% and 0.67%, respectively. A total of 1,027,651 microsatellite motifs were identified and dinucleotide repeat was the most dominant simple sequence repeat (SSR) motif with a frequency of 54.35%. As a by-product of whole genome sequencing, the mitochondrial genome is a powerful tool to investigate the evolutionary relationships between H. nehereus and its relatives. The maximum likelihood (ML) phylogenetic tree was constructed according to the concatenated matrix of amino acids translated from the 13 protein-coding genes (PCGs). Monophyly of two species of the genus Harpadon was revealed in the present study and they formed a monophyletic clade with Saurida with a high bootstrap value of 100%. The results would help to push back the frontiers of genomics and open the doors of molecular diversity as well as conservation genetics studies on this species.
Highlights
Harpadon nehereus (Hamilton, 1822), known as Bombay duck or nomei fish, is generally distributed in the estuarine and nearshore shallow waters of the Indian Ocean and the Western Pacific Ocean [1]
After sequen3c.eRfeisltueltrsing and correction, a total of 68.74 Gb high-quality data were generated by the I3l.1lu
We reported the genome survey of an important economic lizardfish, Bombay duck, using the whole genome sequencing (WGS) method for the first time
Summary
Harpadon nehereus (Hamilton, 1822), known as Bombay duck or nomei fish, is generally distributed in the estuarine and nearshore shallow waters of the Indian Ocean and the Western Pacific Ocean [1]. As a familiar marine lizardfish, H. nehereus is welcomed by consumers for its delicious taste and high nutritional value. It is admeasured that the protein content reaches up to 70% of the dry weight and the calcium content ranges from 1500 to 2500 mg/100 g [2]. Nowadays, it is one of the most important commercial fisheries along the coast of southeast China, Pakistan, India and the Bay of Bengal region [3,4,5,6]. It is necessary to strengthen protection of this fishery in a sustainable way, and further ensure rational exploitation and continued utilization of H. nehereus resources
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