Unzipping haplotypes in diploid and polyploid genomes

Xingtan Zhang; Ruoxi Wu; Yibin Wang; Jiaxin Yu; Haibao Tang

doi:10.1016/j.csbj.2019.11.011

Unzipping haplotypes in diploid and polyploid genomes

Comput Struct Biotechnol J. 2019 Dec 9:18:66-72. doi: 10.1016/j.csbj.2019.11.011. eCollection 2020.

Authors

Xingtan Zhang^{1

2}, Ruoxi Wu¹, Yibin Wang¹, Jiaxin Yu¹, Haibao Tang¹

Affiliations

¹ Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
² State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Abstract

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.

Keywords: Genome assembly; Haplotype phasing; Heterozygosity; Ploidy; Reference genome.

Publication types

Review