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. 2023 Aug 25;10(1):565.
doi: 10.1038/s41597-023-02481-9.

The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps

Sandhya Sukumaran  1 , Wilson Sebastian  2 , A Gopalakrishnan  2 , Oommen K Mathew  3 , V G Vysakh  2 , Prathibha Rohit  2 , J K Jena  2
Affiliations

The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps

Sandhya Sukumaran et al. Sci Data. .

Abstract

The Indian oil sardine, Sardinella longiceps, is a widely distributed and commercially important small pelagic fish of the Northern Indian Ocean. The genome of the Indian oil sardine has been characterized using Illumina and Nanopore platforms. The assembly is 1.077 Gb (31.86 Mb Scaffold N50) in size with a repeat content of 23.24%. The BUSCO (Benchmarking Universal Single Copy Orthologues) completeness of the assembly is 93.5% when compared with Actinopterygii (ray finned fishes) data set. A total of 46316 protein coding genes were predicted. Sardinella longiceps is nutritionally rich with high levels of omega-3 polyunsaturated fatty acids (PUFA). The core genes for omega-3 PUFA biosynthesis, such as Elovl 1a and 1b,Elovl 2, Elovl 4a and 4b,Elovl 8a and 8b,and Fads 2, were observed in Sardinella longiceps. The presence of these genes may indicate the PUFA biosynthetic capability of Indian oil sardine, which needs to be confirmed functionally.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
A photograph of the Indian oil sardine, Sardinella longiceps used for whole genome sequencing.
Fig. 2
Fig. 2
Maximum likelihood phylogenetic tree generated using single copy orthologous genes from 13 representative teleosts and Sardinella longiceps. Lepistosteus aculeatus was used as an outgroup. The tree was generated using IQ-TREE v 2.1.4.
Fig. 3
Fig. 3
(a) Comparison of the Elovl 1 protein of Sardinella longiceps with selected species and maximum likelihood phylogenetic tree constructed using these sequences (b) Comparison of Fads 6 protein of Sardinella longiceps with selected species and maximum likelihood phylogenetic tree constructed using these sequences. The tree was generated using IQ-TREE v 2.1.4.
See this image and copyright information in PMC

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