SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers

文献类型： 外文期刊

第一作者： Jia, Kai-Hua

作者： Jia, Kai-Hua;Xu, Fang-Ji;Li, Guowei;Jia, Kai-Hua;Jiao, Si-Qian;Zhou, Shan-Shan;Liu, Hui;Zhao, Wei;Mao, Jian-Feng;Wang, Zhao-Xuan;Wang, Longxin;Li, Guang-Yuan;Zhang, Wei;Zhang, Ren-Gang;Wang, Xiao-Ling;Wang, Xiao-Ling;Ma, Yongpeng;Bi, Guiqi;El-Kassaby, Yousry A.;Porth, Ilga

作者机构：

关键词： allopolyploids; k-mer; phasing; subgenome; SubPhaser

期刊名称：NEW PHYTOLOGIST （ 影响因子：10.323； 五年影响因子：10.768 ）

ISSN： 0028-646X

年卷期： 2022 年 235 卷 2 期

页码：

收录情况： SCI

摘要： With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

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[1]SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers. Jia, Kai-Hua,Xu, Fang-Ji,Li, Guowei,Jia, Kai-Hua,Jiao, Si-Qian,Zhou, Shan-Shan,Liu, Hui,Zhao, Wei,Mao, Jian-Feng,Wang, Zhao-Xuan,Wang, Longxin,Li, Guang-Yuan,Zhang, Wei,Zhang, Ren-Gang,Wang, Xiao-Ling,Wang, Xiao-Ling,Ma, Yongpeng,Bi, Guiqi,El-Kassaby, Yousry A.,Porth, Ilga. 2022

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