Epigenetic modification brings new opportunities for gene capture by transposable elements in allopolyploid Brassica napus

Abstract

Polyploids are widespread in plants and are important drivers for evolution and biodiversity. Allopolyploidy activates transposable elements (TEs) and causes genomic shock. Plant genomes can regulate gene expression by changing the epigenetic modification of TEs, but the mechanism for TEs to capture genes remains to be explored. Helitron TEs used the 'peel-and-paste' mechanism to achieve gene capture. We identified 3156 capture events and 326 donor genes of Helitron TEs in Brassica napus (A_nA_nC_nC_n). The donor genes captured by TEs were related to the number, length, and location of their exons. The gene-capturing TEs carrying donor gene fragments were evenly distributed on the genome, and more than half of them were involved in the construction of pseudogenes, becoming the reserve force for polyploid evolution. Gene fragment copies enhanced information storage, providing opportunities for gene mutation and the formation of new genes. Simultaneously, the siRNAs targeting TEs may act on the donor genes due to siRNA crosstalk, and the gene methylation levels increased and the expression levels decreased. The genome sought a balance between sacrificing donor gene expression and silencing TEs, allowing TEs to hide in the genome. In addition, epigenetic modifications may temporarily relax the control of gene capture during allopolyploidization. Our study identified and characterized gene capture events in B. napus, analyzed the effects of DNA methylation and siRNA on gene capture events, and explored the regulation mechanism of gene expression by TE epigenetic modification during allopolyploidization, which will contribute to understanding the formation and evolution mechanism of allopolyploidy.

Figure 1

Characteristics of donor genes and gene-capturing TEs in B. napus. (A) Length of donor and random free gene exons. (B) The number of donor and random free gene exons. The squares represented the mean value. Significant differences between donor and free gene exons, using the Wilcoxon test (^***P < 0.001). (C) The proportion of captured exons. (D) Distribution density of all genes, gene-capturing TEs and free TEs on chromosomes of B. napus genome. (E) Repeat motif prediction of captured exons. (F) Repeat motif prediction of gene-capturing TEs.

Figure 2

The fate of genes captured by TEs. (A) The synonymous substitution values of homoeologous genes. (B) The Ka/Ks ratios of the homoeologous gene pairs. (C) The position relationship between gene exons and TEs during capture events. (D) The relationship between the number of donor genes and gene-capturing TEs, and the chromosome length. The Y-axis on the left side of the graph represented the number of donor genes and gene-capturing TEs, and the chromosome length was displayed on the right. (E) The proportion of the relationship between the gene-capturing TEs and captured regions.

Figure 3

The siRNA abundance of gene-capture events in three genotypes of B. napus. (A) Average siRNA abundance of donor and free genes. (B) Average siRNA abundance of gene-capturing and free TEs. (C) The siRNA abundance of captured fragments in gene-capturing TEs and donor genes. (D) The proportion of donor and free genes was regulated by DEsiRNA. (E) The proportion of DEsiRNA in gene-capturing and free TEs during the process of allopolyploidy.

Figure 4

The DNA methylation of gene-capture events in three genotypes of B. napus. (A) Whole methylation levels of donor and free genes. (B) Whole methylation levels of gene-capturing and free TEs. (C) DNA methylation profiles of donor genes, free genes, and their upstream and downstream 2 kb. (D) DNA methylation profiles of gene-capturing TEs, free TEs, and their upstream and downstream 2 kb. (E) The CG, CHG, and CHH methylation of captured fragments in gene-capturing TEs and donor genes. (F) The proportion of DML in donor and free genes. (G) The proportion of DML gene-capturing and free TEs.

Figure 5

Gene expression levels in capture events during allopolyploidization. (A) Average expression levels of donor and free genes in B. napus. (B) The overlap of differential expressed donor and free genes among three comparison groups. (C) The proportion of DEGs to donor and free genes in the three comparison groups. (D) The proportion of expression level up and down of DEGs in donor and free genes.

Figure 6

Epigenetic modification profiles of homoeologous genes with gene capture. (A) The proportion of donor genes in homoeologous and nonhomoeologous genes. (B) The overlap of homoeologous gene pairs between A_n and C_n subgenomes where the donor gene was located. (C) The siRNA abundance of homoeologous genes. (D) The CG, CHG, and CHH methylation levels of homoeologous genes. In (C) and (D), the horizontal coordinate represented the A_n/C_n subgenome where the donor gene was located of homoeologous gene pair in the different genotypes (Wilcoxon test; ^*P < 0.05, ^**P < 0.01, ^***P < 0.001).