Genome Sequence of the White Shark Carcharodon carcharias: Insights into Genome Size Evolution, Life History Characters, and a Primitive Adaptive Immune System.

The white shark, Carcharodon carcharias, is a species of great interest to the public, shark biologists, and geneticists alike.  Several of its life history characteristics are of evolutionary and/or ecological interest such as regional endothermy, its role as a large apex predator, long lifespan, and a primitive adaptive immune system. We have utilized a combination of quality trimmed single-end, paired-end, overlapping paired-end, and mate-paired Illumina sequencing data to obtain 104x coverage of the white shark genome, the largest chondrichthyan genome yet sequenced.  In addition to estimating genome size (5.03 gbp) and repeat content (roughly 60% is comprised of repetitive content), we have employed the MAKER pipeline on the assembled data to provide annotations, resulting in 34,208 predicted genes with an average size of 20.6 kbp.  From these annotated loci we were able to gain insights into the genetics behind several aspects of white shark biology.  For example, sharks are thought to lack color vision.  Accordingly, we were unable to identify the full complement of 5 traditional opsin genes needed for full color vision.  However, genes for two possible color-absorbing opsins were identified and point to the possibility of limited color vision in this species.  We also identified 193,576 microsatellites (23,586 perfect repeats) that could be adapted for conservation genetics studies in this and other lamnid species.  Ongoing study of these genes, those encoding aspects of the adaptive immune system, and telomere length in this species, include some of the current efforts underway with this genome assembly and characterization.