Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

Abstract

Allopolyploidisation merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is 'dominant' over the other subgenome, often being more highly expressed. Here, we 'replayed the evolutionary tape' with six isogenic resynthesised Brassica napus allopolyploid lines and investigated subgenome dominance patterns over the first 10 generations postpolyploidisation. We found that the same subgenome was consistently more dominantly expressed in all lines and generations and that >70% of biased gene pairs showed the same dominance patterns across all lines and an in silico hybrid of the parents. Gene network analyses indicated an enrichment for network interactions and several biological functions for the Brassica oleracea subgenome biased pairs, but no enrichment was identified for Brassica rapa subgenome biased pairs. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the dominant subgenome in all lines and generations. Many of these differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting that subgenome dominance is partly related to parental genome differences rather than just a byproduct of allopolyploidisation. These findings demonstrate that 'replaying the evolutionary tape' in an allopolyploid results in largely repeatable and predictable subgenome expression dominance patterns.

Keywords: Brassica napus; DNA methylation; genomic shock; hybridisation; polyploidy; rapeseed; subgenome dominance.

Fig. 1

Homoeolog expression bias in resynthesised Brassica napus. Distribution of homoeolog bias in the parent and three generations of line EL100. Red regions indicate BnC‐biased homoeologs with log₂ expression fold change > 3.5 and blue regions indicate BnA‐biased homoeologs with log₂ expression fold change < −3.5.

Fig. 2

Common shared biased homoeolog pairs in resynthesised Brassica napus. UpSet plot showing BnC‐biased homoeologs pairs for generations 1 (a), 5 (b), and 10 (c) that are shared or unique among comparisons across all six lines for the three sampled generations. This analysis was restricted only to homoeolog pairs in 2 : 2 balance in all six lines.

Fig. 3

DNA methylation of genes in resynthesised Brassica napus. Metaplots of CG, CHG and CHH mean weighted methylation of all annotated gene models for generations 1, 5 and 10 assessed using Bisulfite‐seq. The six resynthesised lines are shown in purple, the Brassica oleracea progenitor is shown in red, Brassica rapa progenitor in blue, and the in silico mock polyploid in black. Methylation levels are shown for the transcription start site (TSS′), gene body, transcription termination site (TTS′) and 2 kb upstream and downstream of the TSS and TTS.

Fig. 4

DNA methylation of long‐terminal repeat (LTR) TEs in resynthesised Brassica napus. Metaplots of CG, CHG and CHH mean weighted methylation of all annotated LTR TEs for generations 1, 5 and 10 assessed using Bisulfite‐seq. The six resynthesised lines are shown in purple, the Brassica oleracea progenitor is shown in red Brassica rapa progenitor in blue, and the in silico mock polyploid in black. Methylation levels are shown for the transcription start site (TSS'), gene body, transcription termination site (TTS') and 2 kb upstream and downstream of the TSS and TTS.

Fig. 5

DNA methylation of BnC subgenome genes in resynthesised Brassica napus. Metaplots of CG, CHG and CHH mean weighted methylation of all gene models on the BnC subgenome for generations 1, 5 and 10 assessed using Bisulfite‐seq. The six resynthesised lines are shown in purple, the Brassica oleracea progenitor is shown in red and in silico mock polyploid in black as a visual control for cross‐mapping errors. Methylation levels are shown for the transcription start site (TSS′), gene body, transcription termination site (TTS′) and 2 kb upstream and downstream of the TSS and TTS.

Fig. 6

DNA methylation of BnA subgenome genes in resynthesised Brassica napus. Metaplots of CG, CHG and CHH mean weighted methylation of all gene models on the BnA subgenome for generations 1, 5 and 10 assessed using Bisulfite‐seq. The six resynthesised lines are shown in purple, the Brassica rapa progenitor is shown in blue and in silico mock polyploid in black as a visual control for cross‐mapping errors. Methylation levels are shown for the transcription start site (TSS′), gene body, transcription termination site (TTS′) and 2 kb upstream and downstream of the TSS and TTS.

Fig. 7

DNA methylation of BnC subgenome long‐terminal repeat (LTR) TEs in resynthesised Brassica napus. Metaplots of CG, CHG and CHH mean weighted methylation of all LTR TEs on the BnC subgenome for generations 1, 5 and 10 assessed using Bisulfite‐seq. The six resynthesised lines are shown in purple, the Brassica oleracea progenitor is shown in red and in silico mock polyploid in black as a visual control for cross‐mapping errors. Methylation levels are shown for the transcription start site (TSS′), gene body, transcription termination site (TTS′) and 2 kb upstream and downstream of the TSS and TTS.

Fig. 8

DNA methylation of BnA subgenome long‐terminal repeat (LTR) transposable elements in resynthesised Brassica napus. Metaplots of CG, CHG and CHH mean weighted methylation of all LTR transposable elements on the BnA subgenome for generations 1, 5 and 10 assessed using Bisulfite‐seq. The six resynthesised lines are shown in purple, the Brassica rapa progenitor is shown in blue and in silico mock polyploid in black as a visual control for cross‐mapping errors. The data here show unique and unexpected oscillations for CHG methylation, which may be tracking nucleosomes, but are unlikely to be an artefact as CG and CHH methylation is unaffected. Methylation levels are shown for the transcription start site (TSS′), gene body, transcription termination site (TTS′) and 2 kb upstream and downstream of the TSS and TTS.

Fig. 9

DNA Methylation of biased homoeologs in resynthesised Brassica napus. Average weighted methylation for homoeolog pairs in 2 : 2 dosage for all 16 lines assessed using Bisulfite‐seq. BnC‐biased expressed homoeologs in red and BnA‐biased expressed homoeologs in blue. Results are shown for methylation in CG, CHG and CHH contexts. Methylation levels are shown for the transcription start site (TSS′), gene body, transcription termination site (TTS′) and 2 kb upstream and downstream of the TSS and TTS.