Draft genome sequencing and assembly of Risso's dolphin, <i>Grampus griseus</i>

Senevirathna, Jayan D.M.; Yonezawa, Ryo; Saka, Taiki; Hiramatsu, Yuka; Smith, Ashley Rinka; Igarashi, Yoji; Yoshitake, Kazutoshi; Kinoshita, Shigeharu; Funasaka, Noriko; Asakawa, Shuichi

doi:10.7150/jgen.78761

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J Genomics 2023; 11:9-13. doi:10.7150/jgen.78761 This volume Cite

Research Paper

Draft genome sequencing and assembly of Risso's dolphin, Grampus griseus

Jayan D.M. Senevirathna^1,4✉, Ryo Yonezawa¹, Taiki Saka¹, Yuka Hiramatsu¹, Ashley Rinka Smith¹, Yoji Igarashi², Kazutoshi Yoshitake¹, Shigeharu Kinoshita¹, Noriko Funasaka³, Shuichi Asakawa^1✉

1. Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.
2. Department of Life Sciences and Chemistry, Graduate School of Bioresources, Mie University, Japan.
3. Department of Life Sciences, Graduate School of Bioresources, Mie University, Japan.
4. Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Sri Lanka.

Citation:

Senevirathna JDM, Yonezawa R, Saka T, Hiramatsu Y, Smith AR, Igarashi Y, Yoshitake K, Kinoshita S, Funasaka N, Asakawa S. Draft genome sequencing and assembly of Risso's dolphin, Grampus griseus. J Genomics 2023; 11:9-13. doi:10.7150/jgen.78761. https://www.jgenomics.com/v11p0009.htm

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Abstract

The Risso's dolphin (Grampus griseus) is one of the migratory marine mammals and they have commonly dispersed in tropical and temperate seas. It is a least concerned species in the IUCN red list of threatened species. However, their population size and factors affecting their population structure are unknown. Due to the wide distribution of this species, their populations might be genetically stable and less structured. To support genetic studies on dolphins and other marine mammals, we assembled the draft genome of Risso's dolphin that was found in Japan. The tissue samples were used to extract high molecular DNA and subjected to sequencing by Illumina HiSeq X, Oxford Nanopore MinION, and Bionano Saphyr. The assembled hybrid genome was 75.9% of complete eukaryotic BUSCOs and the genome size was 2.256 Gb with 2.042 Mb of scaffold N50. De novo assembly of this genome by Bionano Saphyr recovered 2.036 Gb total genome map length and structural variations. The gene structures of this draft genome were identified by BRAKER2, and 9947 genes were recovered. The data will be useful for future studies of cetaceans.

Keywords: Cetacean, Dolphin, Genome sequencing, Hybrid genome assembly, Vertebrate genomes

Citation styles

APA

Senevirathna, J.D.M., Yonezawa, R., Saka, T., Hiramatsu, Y., Smith, A.R., Igarashi, Y., Yoshitake, K., Kinoshita, S., Funasaka, N., Asakawa, S. (2023). Draft genome sequencing and assembly of Risso's dolphin, Grampus griseus. Journal of Genomics, 11, 9-13. https://doi.org/10.7150/jgen.78761.

ACS

Senevirathna, J.D.M.; Yonezawa, R.; Saka, T.; Hiramatsu, Y.; Smith, A.R.; Igarashi, Y.; Yoshitake, K.; Kinoshita, S.; Funasaka, N.; Asakawa, S. Draft genome sequencing and assembly of Risso's dolphin, Grampus griseus. J. Genomics 2023, 11, 9-13. DOI: 10.7150/jgen.78761.

NLM

CSE

Senevirathna JDM, Yonezawa R, Saka T, Hiramatsu Y, Smith AR, Igarashi Y, Yoshitake K, Kinoshita S, Funasaka N, Asakawa S. 2023. Draft genome sequencing and assembly of Risso's dolphin, Grampus griseus. J Genomics. 11:9-13.

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