De novo phasing resolves haplotype sequences in complex plant genomes

编号 040034704

推送时间 20220613

研究领域 森林培育 

年份 2022 

类型 期刊 

语种 英语

标题 De novo phasing resolves haplotype sequences in complex plant genomes

来源期刊 Plant Biotechnology Journal

期 第347期

发表时间 20220325

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

摘要 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 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.

服务人员 孙小满

服务院士 尹伟伦

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