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

J. Tahir, R. Crowhurst, S.E. Gardiner, I. Liachko, D. Chagné, S. Sullivan, Z. Hanley
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.
Tahir, J., Crowhurst, R., Gardiner, S.E., Liachko, I., Chagné, D., Sullivan, S. and Hanley, Z. (2018). Assembling the genome of a female Actinidia chinensis genotype using proximity-based chromosomal interactions generated from the genome of a male A. chinensis. Acta Hortic. 1218, 81-90
DOI: 10.17660/ActaHortic.2018.1218.10
https://doi.org/10.17660/ActaHortic.2018.1218.10
chromosome conformation capture technique, Hi-C, proximity-guided genome assembly (PGA), 3D structural organization
English

Acta Horticulturae