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

Abstract

Summary 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.

High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry

“…unravelled the complex ancestry and domestication history of cultivated strawberry and found that nucleotide diversity and heterozygosity were significantly lower in cultivated strawberries [ 15 ]. But the hypothesis on hybrid ancestry of octoploid cultivated strawberry was controversial [ 16 , 17 ]. Cauret et al .…”

Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes

“…2–4 and Supplementary Figs 27 – 34 ). Leveraging the recent developments in subgenome-phasing method published by Jia et al 4 , we propose an alternative model, i.e., reticulate allopolyploidization, to account for the evolution and the genomic diversity of these three Papaver species. Our hypothesis is supported by the following lines of evidence: We extracted 4,791 anchor genes from the inter-genomic syntenic blocks at a ratio of 1:2:4 in P. rhoeas , P. somniferum and P. setigerum using OrthoFinder v2.3.1 5 and MCScanX 6 (Supplementary Figs.…”

“…The 95% confidence intervals (CI) of the insertion times are used to infer the time boundary of divergence to hybridization period. We phased the subgenomes of P. somniferum and P. setigerum using SubPhaser v1.2 4 (Supplementary Fig. 1B, C , Supplementary Figs.…”

“…We phased the subgenomes of P. somniferum and P. setigerum using SubPhaser v1.2 4 (Supplementary Fig. 1B, C , Supplementary Figs.…”

Reply to “Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes”

“…We assembled genomes of three Papaver species, P. somniferum, P. rhoeas and P. setigerum , and revealed two-round whole genome duplication (WGD) events and the punctuated patchwork evolution of morphinan and noscapine biosynthesis pathway based on comparative genomic analyses of collinearity, phylogenetic tree, and synonymous substitution rate ( Ks ) at species level 1 . Recently, Zhang et al reanalyzed our three Papaver genomes based on the subgenome-phasing analysis by their newly published tool SubPhaser 2 . They confirmed the two WGDs we previously detected, but provide strong evidence that the WGDs were likely allopolyploidy events.…”