Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond

Abstract

Hybridization has been widely used in breeding of cultivated species showing low genetic variability, such as peach (Prunus persica). The merging of two different genomes in a hybrid often triggers a so-called "genomic shock" with changes in DNA methylation and in the induction of transposable element expression and mobilization. Here, we analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in an F1 hybrid using high-throughput sequencing technologies. Contrary to the "genomic shock" expectations, we found that the overall levels of DNA methylation in the transposable elements in the hybrid are not significantly altered compared with those of the parental genomes. We also observed that the levels of transcription of the transposable elements in the hybrid are in most cases intermediate as compared with that of the parental species and we have not detected cases of higher transcription in the hybrid. We also found that the proportion of genes whose expression is altered in the hybrid compared with the parental species is low. The expression of genes potentially involved in the regulation of the activity of the transposable elements is not altered. We can conclude that the merging of the two parental genomes in this Prunus persica x Prunus dulcis hybrid does not result in a "genomic shock" with significant changes in the DNA methylation or in the transcription. The absence of major changes may facilitate using interspecific peach x almond crosses for peach improvement.

Figure 1

Distribution of the DNA methylation levels in the transposable elements. Violin plots for the distribution of mean methylation levels (expressed in percentage) for different methylation sites (CG, CHG and CHH) in transposable elements of the genomes of almond (A, in green), peach (P, in orange) and the interspecific hybrid (H, in blue). H (A) and H (P) represent the methylation levels of the hybrid computed using Almond or Peach genome, respectively. Statistical significance of the differences between parentals and the hybrid is presented (Wilcoxon test p-value), along with the mean methylation differences (average % of methylation in the hybrid minus average % of methylation in the parental). The numbers in the bottom represent the total number of elements analysed in each case.

Figure 2

Distribution of the DNA methylation levels in the transposable elements separated by categories. Violin plots for the distribution of mean methylation levels (expressed in percentage) for different methylation sites (CG, CHG and CHH) in different classes of transposable elements separately (LTR retrotransposons, LINEs, MITEs and TIRs) in the genomes of almond (A, in green), peach (P, in orange) and the hybrid (H, in blue). H (A) and H (P) represent the methylation levels of the hybrid computed using Almond or Peach genome, respectively. Statistical significance of the differences between parentals and the hybrid is presented (Wilcoxon test p-value). The numbers in the bottom represent the total number of elements analysed in each case.

Figure 3

Differentially methylated regions in LTR retrotransposons when comparing peach and hybrid genomes. Methylation levels of DMRs in the LTR retrotransposon families comparing peach with the hybrid in CHG (A) and CHH (B) contexts. Blue dots indicate that the DMR is more methylated in the hybrid. Orange dots indicate that the DMR is more methylated in peach. Only families with at least 5 DMRs are shown.

Figure 4

Transcriptomic analysis of transposable elements in leaves of almond, peach and the hybrid. A) Patterns of transcription of the TE families. Vertical higher position indicates more transcription (P, peach; H, hybrid; A, almond). Total means the total number of families in peach and almond genomes containing at least one full-length element. B) Heat-map of the transcription levels of the TE families showing expression in at least one of the genotypes. Higher expression is indicated in red and lower expression in dark blue. We show the results of three replicates per sample.

Figure 5

Transcription of LTR retrotransposon families in leaves of almond, peach and the hybrid. Transcription levels of LTR retrotransposons in leaves of almond (A, green), peach (P, orange) and the F1 hybrid (H, blue) analysed by qRT-PCR and RNA-seq. The LTR retrotransposon family is indicated in the top.

Figure 6

Transcription of genes in leaves of almond, peach and the hybrid. Transcriptomic analysis of the genes in leaves of almond, peach and the hybrid. A) Patterns of transcription of the genes. Vertical higher position indicates more transcription (P, peach; H, hybrid; A, almond). B) Average transcription levels of the genes showing significant differential expression in peach, the F1 hybrid and almond. Higher expression is indicated in red and lower expression in dark blue.