Determination of the mutation rate in shark

突变率是生态学和进化、遗传学和基因组学中许多计算和预测建模的关键参数。尽管其重要性，迄今为止，脊椎动物的突变率的实验测定仅在四种哺乳动物物种中完成，即捕蝇草和鲱鱼。鲨鱼在脊椎动物生命树中占有独特的地位，是水生生态系统的重要组成部分。鲨鱼被渔业过度开发，鲨鱼软骨因其癌症发病率低的毫无根据的推断而成为著名的“预防癌症”膳食补充剂。1992年的一项基于线粒体DNA序列的研究表明，鲨鱼可能是一个“缓慢的分子钟谱系”，如果这是真的，将对我们理解这一基础脊椎动物群体的进化，生态学，基因组学以及最后并非最不重要的癌症发展产生巨大影响。然而，这从来没有被跟踪，更重要的是，核突变率是未知的。为了确定全基因组突变率，深度测序方法现在允许使用基于谱系的突变累积方法。我们建议通过使用两代系谱的全基因组测序来确定鲨鱼的突变率。我们处于独特的位置，拥有来自肩章鲨（Hemiscyllium ocellatum）父母及其后代的材料。我们将使用10X Genomics管道对父母及其后代的5.4 Gb基因组进行测序，覆盖率约为60倍，并按照先前成功使用的严格生物信息学程序调用SNP。 将检测从头突变并用于计算核全基因组突变率。亲本基因组之一将以甚至更高的质量水平生成，作为用于比对家族组的测序读段的参考基因组。将通过长读技术（PacBio）和Bionano作图建立参考，以获得最高的邻接度。基因组将被注释，然后用于分析鲨鱼谱系的基因和基因组进化。特别令人感兴趣的是已知在肿瘤中通常受影响的基因和那些被认为可以预防癌症的基因。从雄性和雌性鲨鱼的基因组的可用性也将允许启动在这组脊椎动物的性别决定和发展的研究，迄今为止，这类信息不存在。总之，我们可以期望有助于更好地了解脊椎动物的基因组进化的一般和破译鲨鱼的特殊适应和独特的生物学特征的遗传和基因组基础。

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.