文献类型： 外文期刊

作者： Jia, Kai-Hua ¹ ; Wang, Zhao-Xuan ³ ; Wang, Longxin ⁴ ; Li, Guang-Yuan ⁵ ; Zhang, Wei ⁵ ; Wang, Xiao-Ling ⁶ ; Xu, Fang-Ji ¹ ; Jiao, Si-Qian ² ; Zhou, Shan-Shan ² ; Liu, Hui ² ; Ma, Yongpeng ⁸ ; Bi, Guiqi ⁹ ; Zhao, Wei ² ; El-Kassaby, Yousry A. ¹⁰ ; Porth, Ilga ¹¹ ; Li, Guowei ¹ ; Zhang, Ren-Gang ⁵ ; Mao, Jian-Feng ² ;

作者机构： 1.Shandong Acad Agr Sci, Inst Crop Germplasm Resources, Key Lab Crop Genet Improvement & Ecol & Physiol, Jinan 250100, Peoples R China

2.Beijing Forestry Univ, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Coll Biol Sci & Technol,Natl Engn Res Ctr Tree Br, Minist Educ,Key Lab Genet & Breeding Forest Trees, Beijing 100083, Peoples R China

3.Shijiazhuang Peoples Med Coll, Shijiazhuang 050091, Hebei, Peoples R China

4.Univ Jinan, Sch Biol Sci & Technol, Jinan 250022, Peoples R China

5.Ori Shandong Gene Sci & Technol Co Ltd, Dept Bioinformat, Weifang 261322, Peoples R China

6.BGI Shenzhen, Shenzhen 518083, Peoples R China

7.Univ Chinese Acad Sci, BGI Educ Ctr, Shenzhen 518083, Peoples R China

8.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Integrat Conservat Plant Species E, Kunming 650201, Yunnan, Peoples R China

9.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen,Genome Anal Lab, Minist Agr & Rural Affairs,Shenzhen Key Lab Agr S, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr, Shenzhen 518124, Peoples R China

10.Univ British Columbia, Fac Forestry, Dept Forest & Conservat Sci, Vancouver, BC V6T 1Z4, Canada

11.Univ Laval, Fac Foresterie Geog & Geomat, Dept Sci Bois & Foret, Quebec City, PQ G1V 0A6, Canada

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.