De novo Assembly and Analysis of a Korean Native Pig, Chookjin Chamdon

Chookjin Chamdon is one of the indigenous pig breeds in Korea peninsula registered with Food and Agricultural Organization. The native pig is known to have peculiar meat qualities appealing to Korean consumers. The population size of Chookjin Chamdon has been severely reduced mainly due to the extensive cross-breeding with European breeds to improve its productivity since the beginning of the 20th century. As many local livestock breeds across the world, the Chookjin Chamdon has not been well investigated particularly in the whole-genome level. We sequenced the genome of a male Chookjin Chamdon using Illumina HiSeq 2000 and Roche 454 pyrosequencing platforms. AllPaths-LG was used to assemble the generated sequence reads, followed by gap filling and then scaffolds were furthermore curated and rearranged using the reference-assisted chromosome Assembly pipeline. As a result, a total of 357 scaffolds were generated corresponding to 2.52 Gbp with a mean scaffold size of 7 Mbp and N50 size of 17.2 Mbp. Those scaffolds cover approximately 95% of the swine reference genome assembly (Sscrofa 10.2). We also predicted and annotated 21,643 genes and approximately 5.4 million repeat elements masking 40.7 % (986 Mbp) of the Chookjin Chamdon assembly. In addition, the results from the de novo sequencing were compared with the Sus sucrofa reference genome assembly, and the differences from the comparison were further supported by whole-genome resequencing of multiple individuals of Chookjin Chamdon. We expect our study will be a good resource for genome-wide comparative genomics between pig breeds.