Determination of the mutation rate in shark

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The mutation rate is a crucial parameter for many calculations and predictive modellings in ecology and evolution, genetics and genomics. Despite its importance, so far experimental determination of mutation rates in vertebrates has only been accomplished in four mammalian species, flycatcher and herring. Sharks hold a unique position in the vertebrate tree of life and are important components of aquatic ecosystems. They are overexploited by fisheries and shark cartilage became famous as a "cancer-prevention" dietary supplement based on the unfounded extrapolation of the low cancer rate in sharks. A mitochondrial DNA sequences based study in 1992 indicated that sharks might be a "slow molecular clock lineage", which - if true - would have enormous consequences for our understanding of the evolution, ecology, genomics and last not least cancer development in this basal vertebrate group. However, this has never been followed up and even more importantly, the nuclear mutation rate is unknown. For determining genome-wide mutation rates, the deep sequencing methodologies now allow to use a pedigree based mutation accumulation approach. We propose to determine the mutation rate in sharks by using whole genome sequencing of a two-generation pedigree. We are in the unique position to have material from both parents and their offspring of the Epaulette shark (Hemiscyllium ocellatum). We will sequence the 5.4 Gb genomes of both parents and their offspring to about 60x coverage with the 10X Genomics pipeline and call SNPs following the stringent bioinformatic procedures successfully used previously. De novo mutations will be detected and used to calculate the nuclear genome-wide mutation rate. One of the parent genomes will be generated on an even higher quality level as reference genome for aligning the sequencing reads of the family panel. The reference will be established by long read technology (PacBio) and Bionano mapping for highest contiguity. The genome will be annotated and then used to analyse gene and genome evolution in the shark lineage. Of particular interest are genes that are known to be commonly affected in tumours and those that are considered to protect from cancer. The availability of genomes from a male and a female shark will also allow to initiate research on sex determination and development in this group of vertebrates where so far no such information exists.In summary, we can expect to contribute to a better understanding of vertebrate genome evolution in general and to decipher the genetic and genomic basis of special adaptations and peculiar biological features of sharks.