High coverage of the complete mitochondrial genome of the rare Gray’s beaked whale (Mesoplodon grayi) using Illumina next generation sequencing

Abstract

Using an Illumina platform, we shot-gun sequenced the complete mitochondrial genome of Gray’s beaked whale (Mesoplodon grayi) to an average coverage of 152X. We performed a de novo assembly using SOAPdenovo2 and determined the total mitogenome length to be 16,347 bp. The nucleotide composition was asymmetric (33.3% A, 24.6% C, 12.6% G, 29.5% T) with an overall GC content of 37.2%. The gene organization was similar to that of other cetaceans with 13 protein-coding genes, 2 rRNAs (12S and 16S), 22 predicted tRNAs and 1 control region or D-loop. We found no evidence of heteroplasmy or nuclear copies of mitochondrial DNA in this individual. Beaked whales within the genus Mesoplodon are rarely seen at sea and their basic biology is poorly understood. These data will contribute to resolving the phylogeography and population ecology of this speciose group.

• Annotation
• assembly
• cetacea
• mitochondrial genome

Acknowledgements

The authors would like to thank the following: Lester Bridson of the New Zealand Department of Conservation; New Zealand Genomics Ltd; the Centre for Genomics, Proteomics and Metabolomics; the New Zealand Cetacean Tissue Archive at the University of Auckland.

Declaration of interest

This study was supported by funding from University of Auckland. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.