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Genomic Characteristics of Okamejei kenojei and the Implications to Its Evolutionary Biology Study

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Abstract

Okamejei kenojei is an important economic species widely distributed in shallow coastal waters of the western North Pacific. In this study, the whole-genome survey analysis of O. kenojei was conducted to reveal its genomic characteristics. The genome size was estimated to be 2027.44 Mb, the repeat sequence content was 44.90%, and the heterozygous ratio was 1.04%. The mitochondrial genome excavated from the sequencing data was 16,974 bp, and it can form the closed circular molecule. The phylogenetic tree based on 13 protein-coding gene sequences supported the validity of Okamejei and assisted the conclusion that Raja porosa was the junior synonym of O. kenojei. Plenty of potential microsatellite loci were identified, and the distribution frequency was estimated to be approximately 236.3 SSRs per Mb. Among all motif types of microsatellites, the dinucleotide repeats were dominant (82.59%), followed by the trinucleotide repeats (8.05%), tetranucleotide repeats (5.80%), pentanucleotide repeats (2.83%), and hexanucleotide repeats (0.72%). The results of the present study could not only provide useful information for understanding the genome structure and functional characteristics of O. kenojei, but also lay the foundation for the subsequent mapping of the whole genome.

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Data Availability

The whole-genome data have been uploaded to National Center for Biotechnology Information (NCBI), and the BioProject ID is PRJNA977198.

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Acknowledgements

We would like to express deep appreciation to Dr. Chi Zhang from Ocean University of China for identifying species.

Funding

This study is supported by the opening foundation of the Observation and Research Station of Bohai Strait Eco-Corridor, MNR (BH202203).

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Authors and Affiliations

  1. The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, Shandong, China

    Na Song, Siyu Ma, Xiang Zhao & Jiabao Zhao

  2. Ministry of Natural Resources, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Qingdao, 266061, Shandong, China

    Linlin Zhao

Authors
  1. Na Song
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  2. Siyu Ma
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  3. Xiang Zhao
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  4. Jiabao Zhao
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Contributions

Na Song and Linlin Zhao conceived and designed the experiments. Siyu Ma performed the experiments. Siyu Ma and Xiang Zhao analyzed the data. Jiabao Zhao contributed chart organization. Na Song and Linlin Zhao wrote the main manuscript text. Siyu Ma, Xiang Zhao, and Jiabao Zhao revised the manuscript.

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Correspondence to Linlin Zhao.

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Song, N., Ma, S., Zhao, X. et al. Genomic Characteristics of Okamejei kenojei and the Implications to Its Evolutionary Biology Study. Mar Biotechnol 25, 815–823 (2023). https://doi.org/10.1007/s10126-023-10242-3

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