In:
New Phytologist, Wiley, Vol. 235, No. 2 ( 2022-07), p. 801-809
Abstract:
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, S ub P haser , specifically designed for a neoallopolyploid or a homoploid hybrid. S ub P haser 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. S ub P haser 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 S ub P haser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, S ub P haser , 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.
Type of Medium:
Online Resource
ISSN:
0028-646X
,
1469-8137
Language:
English
Publisher:
Wiley
Publication Date:
2022
detail.hit.zdb_id:
208885-X
detail.hit.zdb_id:
1472194-6
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