Improving the Pig Genome Assembly with Mate-Pair Sequences

Most of the -omics projects rely on the availability of an accurate reference genomic sequence. In this study, we performed mate-pair sequencing experiments on pig (Sus scrofa) DNA samples with two objectives:
- Improve the assembly of the reference genome.
- Identify breed-specific structural variations to investigate the genome plasticity.

In this report we present an improved version of the pig genome that results from re-assembling the existing contigs with mate-pair data. By using the Illumina Nextera protocol we sequenced the extremities of ~6Kb-long genomic fragments. Resulting mate-pair sequences were then used to connect contigs into pairs and redefine their relative order and orientation within each chromosome.

We show how the assembly can be improved in terms of number of scaffolds, consistency with the experimental data and comparative genomics. We also illustrate the importance of a high-quality reference assembly for the identification of structural variants from mate-pair data.