Elephant shark genome

Cartilaginous fishes (Chondrichthyes) are the phylogenetically oldest group of living jawed vertebrates (gnathostomes) and thus constitute an important group for understanding the origin of complex developmental and physiological systems in jawed vertebrates. They are also a useful outgroup to bony vertebrates (comprising ray-finned fishes, lobe-finned fishes and tetrapods) and can help in identifying specialized features that have led to the evolution of diverse groups of bony vertebrates. Cartilaginous fishes differ from bony vertebrates mainly by possessing a largely cartilaginous endoskeleton and lacking bone. There are about 1,000 species of cartilaginous fishes that are divided into two broad groups: the holocephalans (chimaeras) and elasmobranchs (sharks, rays and skates). We proposed elephant shark (Callorhinchus milii), a holocephalan, as a model cartilaginous fish genome because of its smallest genome (~1 Gb) among known cartilaginous fishes. Survey sequencing (1.4× coverage Sanger sequences; accession number AAVX01000000) indicated that unlike teleost fishes, the elephant shark has not experienced an additional round of whole genome duplication, underscoring its importance as a useful reference genome. We have now obtained a whole-genome assembly of the elephant shark using a combination of next-generation and Sanger sequencing. The annotated genome assembly and other resources are presented here.

Assembly statistics

The whole-genome assembly of the elephant shark (accession number AAVX02000000) comprises 67,420 contigs which are assembled into 21,203 scaffolds and cover 937 Mb of the 1-Gb genome of elephant shark. The N50 contig length is 46.6 kb whereas the N50 scaffold length is 4.52 Mb.

Gene content

Protein-coding genes:17,449
Protein-coding transcripts:26,799
Pseudogenes:260
RNA genes:1,099
Repetitive sequences:30%
Average GC content:42%
Acknowledgements

This project is supported by the Biomedical Research Council of A*STAR, Singapore, and the National Human Genome Research Institute (NHGRI), NIH, USA. We thank the A*STAR Computational Resource Centre for their computational support.


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LAST UPDATED: 10-Jan-2014


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