Unzipping haplotypes in diploid and polyploid genomes

Diploid genomes consist of two homologous copies of chromosomes with one from each parent while polyploid genomes contain more than two homologous sets of chromosomes. Most of the reference genome assemblies collapsed haplotypes that represent ‘mosaic’ sequences, ignoring allelic variants that may b...

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Bibliographic Details
Published in:Computational and structural biotechnology journal 2020-01, Vol.18, p.66-72
Main Authors: Zhang, Xingtan, Wu, Ruoxi, Wang, Yibin, Yu, Jiaxin, Tang, Haibao
Format: Article
Language:English
Subjects:
Genome assembly
Haplotype phasing
Heterozygosity
Ploidy
Reference genome
Review
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Summary:Diploid genomes consist of two homologous copies of chromosomes with one from each parent while polyploid genomes contain more than two homologous sets of chromosomes. Most of the reference genome assemblies collapsed haplotypes that represent ‘mosaic’ sequences, ignoring allelic variants that may be involved in important cellular and biological functions. Unzipping haplotypes into distinct sets of sequences has been a growing trend in recent genome studies, as it is an essential tool towards resolving important clinical and biological questions, such as compound heterozygotes, heterosis, and evolution. Herein, we review existing methods for alignment-based and assembly-based haplotype phasing for heterozygous diploid and polyploid genomes, as well as recent advances of experimental approaches for improved genome phasing. We anticipate that full haplotype phasing could become a routine procedure in genome studies in the near future.
ISSN:2001-0370
2001-0370
DOI:10.1016/j.csbj.2019.11.011