Articles
Assembling the genome of a female Actinidia chinensis genotype using proximity-based chromosomal interactions generated from the genome of a male A. chinensis
Article number
1218_10
Pages
81 – 90
Language
English
Abstract
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.
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.
Publication
Authors
J. Tahir, R. Crowhurst, S.E. Gardiner, I. Liachko, D. Chagné, S. Sullivan, Z. Hanley
Keywords
chromosome conformation capture technique, Hi-C, proximity-guided genome assembly (PGA), 3D structural organization
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