Abstract
The marked increase in plant genomic data has provided valuable resources for investigating the dynamic evolution of duplicate genes in polyploidy. Brassica napus is an ideal model species for investigating polyploid genome evolution. The present study comprehensively analyzed DNA and RNA variation of two representative B. napus inbredlines, Zhongshuang11 and Zhongyou821, and we investigated gene expression levels of An and Cn subgenomes in multiple tissues of the two lines. The distribution of transmitted single nucleotide polymorphisms (SNPs) was significantly different in two subgenomes of B. napus. Gene expression levels were significantly negatively correlated with number of variations in replication and transcription of the corresponding genes, but were positively correlated with the ratios of transmitted SNPs from DNA to RNA. We found a higher density of SNP variation in An than that in Cn during DNA replication and more SNPs were transmitted to RNA during transcription, which may contribute to An expression dominance. These activities resulted in asymmetrical gene expression in polyploid B. napus. The SNPs transmitted from DNA to RNA could be an important complement feature in comparative genomics, and they may play important roles in asymmetrical genome evolution in polyploidy.
Highlights
Polyploidy is an important part of the history of natural plant species, and has promoted the domestication of cultivated crop species (Chen et al, 2018)
Among these single nucleotide polymorphisms (SNPs), there were 349,509 SNPs distributed in 40,903 genic regions and 846,691 SNPs located in intergenic regions. 162,124 of the genic SNPs were located in exon regions and 139,244 SNPs in intron regions (Supplementary Table S2)
We identified 792,189 SNPs at the transcription level in ZY821, and most variations were detected in chromosome chrA03 (63,925 SNPs)
Summary
Polyploidy is an important part of the history of natural plant species, and has promoted the domestication of cultivated crop species (Chen et al, 2018). Genome sequencing and comparative genomic analysis have identified ∼50 polyploidization events across plant phylogenetic trees to date (Vanneste et al, 2014; Van de Peer et al, 2017; Chen et al, 2018). Polyploidization is considered the primary driver of plant species diversification and plays an important role in plant genome evolution. Polyploidy has become a popular research topic in plant science due to the increased number of polyploidization events identified in plants. Asymmetric Divergence and Polyploidy Evolution bias and expression dominance between homoeologous genes from different subgenomes, is ubiquitous in polyploidy, especially in allopolyploids. Understanding the mechanism of subgenome dominance has progressed, further investigation is needed to fully understand the subgenome dominance and polyploidy evolution
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