Abstract
Brassica rapa includes some of the most important vegetables worldwide as well as oilseed crops. The complete annotated genome sequence confirmed its paleohexaploid origins and provides opportunities for exploring the detailed process of polyploid genome evolution. We generated a genome-wide DNA methylation profile for B. rapa using a modified reduced representation bisulfite sequencing (RRBS) method. This sampling represented 2.24% of all CG loci (2.5 × 105), 2.16% CHG (2.7 × 105), and 1.68% CHH loci (1.05 × 105) (where H = A, T, or C). Our sampling of DNA methylation in B. rapa indicated that 52.4% of CG sites were present as 5mCG, with 31.8% of CHG and 8.3% of CHH. It was found that genic regions of single copy genes had significantly higher methylation compared to those of two or three copy genes. Differences in degree of genic DNA methylation were observed in a hierarchical relationship corresponding to the relative age of the three ancestral subgenomes, primarily accounted by single-copy genes. RNA-seq analysis revealed that overall the level of transcription was negatively correlated with mean gene methylation content and depended on copy number or was associated with the different subgenomes. These results provide new insights into the role epigenetic variation plays in polyploid genome evolution, and suggest an alternative mechanism for duplicate gene loss.
Highlights
Polyploidy, where more than two complete sets of chromosomes reside within the same nucleus, is both pervasive and ancient in most eukaryotic lineages and is prevalent in plants (Jiao et al, 2011; Proost et al, 2011)
Representative DNA Methylation Profile for the B. rapa Genome In order to generate a representative profile of the global DNA methylation in B. rapa, a modified representation bisulfite sequencing (RRBS) protocol was used (Figure S1), yielding a total of 2.3 Gb PE100 (100 bp paired-end) sequence data
After sequence trimming and filtering, a total of 3.2 million PE75 (0.48 G) high-quality reads were collected. These sequences were aligned to the reference B. rapa Chiifu-401 genome by Bowtie2, and a total of 36,836 candidate SNPs were detected using Samtools
Summary
Polyploidy, where more than two complete sets of chromosomes reside within the same nucleus, is both pervasive and ancient in most eukaryotic lineages and is prevalent in plants (Jiao et al, 2011; Proost et al, 2011). Gene losses within different genomes are usually unequal, with one of the duplicated genomes consistently losing significantly more genes than the others This bias in gene loss was first observed in Arabidopsis (Thomas et al, 2006) and more recently in maize (Woodhouse et al, 2010; Schnable et al, 2011) and Brassica rapa (Wang et al, 2011; Tang et al, 2012), and is probably a general characteristic of major eukaryote lineages where paleopolyploidy has been involved (Sankoff et al, 2010). A monocotyledon species that experienced tetraploidy 5–12 million years ago, biased gene losses between two complete subgenomes are both ancient and ongoing among diverse inbreds, primarily resulting from a mechanism of short deletions (Woodhouse et al, 2010). Differential epigenetic marking of the genomes within an allopolyploid has been suggested as a mechanism underlying differential expression of genes retained in different subgenomes (Schnable et al, 2011; Diez et al, 2014)
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