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Abstract
The sparkling enope squid, Watasenia scintillans, is a deep-sea mollusk inhabiting the western part of the Pacific Ocean. It has the peculiar ability to illuminate its body without the involvement of other organisms. In this study, we extracted the brain DNA from a single squid female caught in the Japan Sea and determined the complete genome sequence of its mitochondrial DNA using the Illumina sequencing platform. The circular sequence is 20,089 bp in length. Using the next-generation sequencing data, we also estimated the mean copy number of mitochondria per cell in the brain to be 108 by comparing the depths of the read data in the nuclear and mitochondrial genomes. The haploid genome size was calculated to be 4.78 Gb. Six heteroplasmy sites were also identified, together with their allele frequencies, in this individual. Our methodology is shown to be useful in mitochondrion-related studies.
Acknowledgements
The authors are grateful to the Hotaruika Museum (Namerikawa, Toyama, Japan) for providing the live squid, including the female sample, Lisette, used in the present study. Computation time was provided by the computer cluster HA8000/RS210 at the Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan.
Declaration of interest
This work was supported by KAKENHI (23770273, 24390251 and 12J05107). The authors declare that they have no competing interests.
Nucleotide sequence accession numbers
The complete sequence of the mitochondrial DNA of W. scintillans has been submitted to GenBank under accession number KJ845633 and the mapped short reads have been submitted to SRA under accession number SRP043307. The sequence variations, including heteroplasmy sites, identified in this study have been submitted to dbSNP under accession numbers ss1052335984–ss1052336004, which will be released as refSNP data in Build 142.