Custom Gap-filling de novo assembly workflow results in improved update of the draft porcine genome v10.2 (Sus scrofa). update of the draft porcine genome v10.2 (Sus scrofa)

An accurate and complete pig genome reference sequence is of essential importance to thestudies of pig biological characteristics and its agricultural traits for pig husbandry. Here, we have carried out a project of next-generation sequencing of 10Duroccloned male piggies and their donor cell line. We obtained 300Gb informative sequencing data. Among the randomly selected contigs, 85% of them were proven to exist by long range confirming PCR. The whole porcine genome size was re-estimated to be about 2.82Gb. 23713 gaps in the reference V10.2 have been filled and the quality of the porcine genome has been improved by increasing the length of the contig N50 from 79kb to 138kb. By de novo assembly, we generated a novel genomic sequence of 338Mbwhich consisted of the unmapped reads of 101,714 contigsto the previously reported pig genome Susscrofa 10.2 (V10.2). The Y chromosome specific contigs were also identified in the 338 Mb sequence by sequence comparisons and confirmed by PCR. As well as, many important genes, associated with cancer trigger or phenotypes change in human or mouse, were found in our de novo sequence data. Our work has given rise to significant improvement to the quality and integrity of the porcine genome.