Assembling the genome of a female Actinidia chinensis genotype using proximity-based chromosomal interactions generated from the genome of a male A. chinensis

The rapid improvement in DNA sequencing technologies is assisting significantly in the assembly of complex genomes. The first draft genome of a female kiwifruit (Actinidia chinensis) was constructed using Illumina paired-end and mate-pair reads, and provided an assembly of 616 Mbp (Huang et al., 2013). The current study evaluates the potential of a chromosome conformation capture technique known as Hi-C to develop an initial draft genome assembly of a diploid kiwifruit. Hi-C captures proximity-based chromosomal interactions to map the 3D structural organization of the genome. The occurrence of proximity interactions is inversely correlated with genomic distance, allowing Hi-C data to be used for genome scaffolding, yielding chromosome-scale assemblies. In preparation for the assembly of a male kiwifruit genome, we have tested the ability of male Hi-C data to scaffold a genome assembly for a female genotype of the same species, which has recently been assembled to chromosomal level using genetic markers to assign scaffolds to linkage groups. The potential of Hi-C-based proximity-guided assembly (PGA) for assisting in the drafting of a genome is discussed.