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. 2020 May 5;11:421. doi: 10.3389/fgene.2020.00421

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Copyright © 2020 Smit, Vivier and Young.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Illustration contrasting the differences in approach between phased diploid (A) and short-read sequencing (B) to generate the diploid and PN40024 reference genomes, respectively. (A) PacBio long-reads (> 30 kb) undergo phasing during the assembly, using FALCON-UNZIP, resulting in the generation of a pseudomolecule known as a primary contig. This primary contig region represents both possible haplotypes. The phasing algorithm identifies reads with high heterozygosity to call an alternate genomic region (haplotig) which is assembled separately allowing for the generation of haplotype regions. (B) The reference genome was generated from an inbred clone of Pinot Noir (PN40024), reducing genomic complexity to near homozygosity. Assembly of the short-reads, generation of contigs and subsequent mapping/assembly to chromosomes lead to the PN40024 reference genome.