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

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

© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.

Détails bibliographiques
Publié dans:The New phytologist. - 1984. - 235(2022), 2 vom: 03. Juli, Seite 801-809
Auteur principal: Jia, Kai-Hua (Auteur)
Autres auteurs: Wang, Zhao-Xuan, Wang, Longxin, Li, Guang-Yuan, Zhang, Wei, Wang, Xiao-Ling, Xu, Fang-Ji, Jiao, Si-Qian, Zhou, Shan-Shan, Liu, Hui, Ma, Yongpeng, Bi, Guiqi, Zhao, Wei, El-Kassaby, Yousry A, Porth, Ilga, Li, Guowei, Zhang, Ren-Gang, Mao, Jian-Feng
Format: Article en ligne
Langue:English
Publié: 2022
Accès à la collection:The New phytologist
Sujets:Journal Article Research Support, Non-U.S. Gov't SubPhaser allopolyploids k-mer phasing subgenome
Description
Résumé:© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.
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
Description:Date Completed 17.06.2022
Date Revised 27.06.2022
published: Print-Electronic
Citation Status MEDLINE
ISSN:1469-8137
DOI:10.1111/nph.18173