The differentiation of homoeologous pairs of chromosomes into subgenome A (blue) and subgenome B (red) based on the hierarchical clustering of Euclidean distances among scaffolds using counts of 13-mers.

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... We found 919 13-mers (13-bp sequences) occurring at least 100 times across the whole genome and also were at least 3-fold enriched in one of the homoeologous chromosomes relative to the other. Based on the consistent enrichment for these 919 13-mers along the putative homoeologous chromosomes, each scaffold of a pair was assigned to a subgenome (Fig. 3). The A group was defined based on the excessive abundance of 773 13-mers and the B group based on the abundance of the other 146 13-mers (Fig. 3). We then computed the densities of A-and B-preferred 13-mers across the scaffolds ( Supplementary Fig. S3A, B) and identified potential homoeologous exchange between subgenomes. Scaffold 8 ...

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... homoeologous chromosomes relative to the other. Based on the consistent enrichment for these 919 13-mers along the putative homoeologous chromosomes, each scaffold of a pair was assigned to a subgenome (Fig. 3). The A group was defined based on the excessive abundance of 773 13-mers and the B group based on the abundance of the other 146 13-mers (Fig. 3). We then computed the densities of A-and B-preferred 13-mers across the scaffolds ( Supplementary Fig. S3A, B) and identified potential homoeologous exchange between subgenomes. Scaffold 8 from the B subgenome had a high density of subgenome A-preferred kmers at one end of the scaffold ( Supplementary Fig. S3B), consistent with the ...

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... A group was defined based on the excessive abundance of 773 13-mers and the B group based on the abundance of the other 146 13-mers (Fig. 3). We then computed the densities of A-and B-preferred 13-mers across the scaffolds ( Supplementary Fig. S3A, B) and identified potential homoeologous exchange between subgenomes. Scaffold 8 from the B subgenome had a high density of subgenome A-preferred kmers at one end of the scaffold ( Supplementary Fig. S3B), consistent with the observation of a translocation from the dot plots (Fig. 2). ...

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... then computed the densities of A-and B-preferred 13-mers across the scaffolds ( Supplementary Fig. S3A, B) and identified potential homoeologous exchange between subgenomes. Scaffold 8 from the B subgenome had a high density of subgenome A-preferred kmers at one end of the scaffold ( Supplementary Fig. S3B), consistent with the observation of a translocation from the dot plots (Fig. 2). We then tested for homoeologous exchange across the subgenomes using a hidden Markov model (HMM) implemented in the R/HMM package [47]. ...

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... with these repeated elements. There were 8 LTR subfamilies (Grande1_ZM_pol/Gypsy, RIRE2_pol/Gypsy, Copia-11_SB/Copia, Copia-73_Mad/Copia, Copia-13_SB/Copia, SZ7_pol/Gypsy, CRM/Gypsy, Atlantys_OS_polGypsy) identified in subgenome A and only 1 (Copia-9_SB/Copia) identified in subgenome B. Their genomic locations are shown in Supplementary Fig. S3C, ...

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... is known for its role in epigenetic gene silencing [51,52,58] and in restricting TE activity [59]. Interestingly, subgenome A also appears to have had more active LTRs at the time of the most recent allopolyploidization event, as evidenced by the greater number of diagnostic kmers and LTR families associated with subgenome A (Supplementary Fig. S3). It would be interesting to explore if the higher LTR activity prior to the WGD (Fig. 4B) and the dominance of subgenome A (Table 4) were related. More retained genes and more active TEs have also been observed in the dominant subgenome of Miscanthus [46], but further investigation into the relationship between TE activity and genome ...

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... initial HMM used equal starting probabilities and transition probabilities of 0.01. We trained the HMM emission probabilities (viterbiTraining) using scaffold 5 and scaffold 15 as they appeared not to be subject to any subgenome exchange based on the A and B k-mer density plots ( Supplementary Fig. S3). ...