4.7 Review

De novo phasing resolves haplotype sequences in complex plant genomes

Journal

PLANT BIOTECHNOLOGY JOURNAL
Volume 20, Issue 6, Pages 1031-1041

Publisher

WILEY
DOI: 10.1111/pbi.13815

Keywords

de novo phasing; haplotype-resolved assembly; autopolyploid; chromosomal rearrangement; haplotype-specific sequence insertion; allele-specific expression; plant genome

Funding

  1. Korea Forest Service of the Korean Government through the R&D Program for Forestry Technology [2014071H10-2022-AA04]
  2. Basic Science Research Program through the National Research Foundation of Korea (NRF) [NRF-2017R1A6A3A04004014]
  3. Korea Forestry Promotion Institute (KOFPI) [2014071H10-2022-AA04] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)

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Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Using haplotype-resolved genome assemblies in plants can reveal significant differences among haplotypes regarding chromosomal rearrangements and expression of specific alleles, contributing to the understanding of biological characteristics of plant species. However, there are limitations in current genome-phasing methods that need to be addressed for further improvements.
Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Because differences between haplotypes are ignored in most published de novo genomes, assemblies are available as consensus genomes consisting of haplotype mixtures, thus increasing the need for genome phasing. Here, we review the operating principles and characteristics of several freely available and widely used phasing tools (TrioCanu, FALCON-Phase, and ALLHiC). An examination of downstream analyses using haplotype-resolved genome assemblies in plants indicated significant differences among haplotypes regarding chromosomal rearrangements, sequence insertions, and expression of specific alleles that contribute to the acquisition of the biological characteristics of plant species. Finally, we suggest directions to solve addressing limitations of current genome-phasing methods. This review provides insights into the current progress, limitations, and future directions of de novo genome phasing, which will enable researchers to easily access and utilize genome-phasing in studies involving highly heterozygous complex plant genomes.

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