A Draft Genome of Korean Native Pig: Current Status and Its Characteristics

De novo genome sequencing of a Korean native pig: current progress and future works Starting from the panda genome sequencing project, genome sequencing using only NGS technology has been widely adapted to mammalian genome sequencing projects. The pig is one of the most important food sources and one of the oldest forms of livestock. Even though two pig breeds, Duroc swine and Mini-pig, were sequenced previously, it is important to sequence local breeds to elucidate their genomic features. Korean native pig assumed to be come to Korea via north China around 2000 years ago. It has long black coarse hair, long straight nose, and small body weight (approximately 70 kg at adult). Here we report the progress of the de novo genome sequencing project to make a reference genome sequence of Korean native pig. We sequenced various kinds of libraries (170 bp, 300 bp, 400 bp, 500 bp and 600 bp insert paired-end; 2 Kbp, 5Kbp, 7Kbp and 10Kbp insert mate-pair) to approximately 136x coverage using Illumina GA IIx and HiSeq 2000 platforms. Small amount of 20Kb long insert library (~0.1x) was sequenced using 454 GS FLX platform. De novo sequence assembly was performed on these sequence sets using AllPaths-LG. After filling gaps using GapCloser in SOAPdenovo2 package, we applied RACA pipeline which curates and rearranges scaffolds using comparative genomic information. This resulted in 357 scaffolds totaling 2.52 Gb with a mean scaffold size of 7 Mb and N50 size of 17.2 Mb covering over 95% of the Duroc swine genome (excluding unplaced scaffolds). The assembly result is superior to the Mini-pig genome’s (1,138,136 scaffolds, N50 size of 5.4 Mb). Korean pig draft genome will be a good resource for genome-wide comparative genomics between pig breeds or novel gene identification.