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Uniparental gene expression, observed in both animals and plants, is termed genomic imprinting. Genomic imprinting is a well-known epigenetic phenomenon regulated through epigenetic modifications such as DNA methylation and histone modifications. Recent genome-wide studies of endosperm transcription have revealed the rapid change of imprinted genes between species, suggesting the flexibility of this phenomenon. Although the functional significance and evolutionary trends of imprinted genes are still obscure, it can be clarified by inter-species comparisons. In this study, we analyzed the pattern of genomic imprinting in Brassica rapa, a species related to Arabidopsis thaliana.
RNA-Seq overview: Two lines of B. rapa (RJKB and OSD) were used in the crossing experiments. Seeds of two strains were sown in soil at the same time. Two independent reciprocal crosses between two strains were conducted in a greenhouse. Seeds of plants 11 days after pollination (DAP) were dissected using a stereomicroscope. Total RNAs were extracted from dissected endosmerms and used for RNA-Seq library preparation. To eliminate genes possibly affected by seed coat contaminations, the differentially expressed gene sets between seed coats and endosperms were estimated. The endosperms and seed coats were sampled from self-crossing of B. rapa strain FPsc to collect enough sample for RNA-Seq of seed coats. The total RNA was extracted from each tissue and sequenced by NextSeq (illumina). We obtained the data of 2 replicates.
Genome sequencing overview: To confirm SNPs sites between two lines (RJKB and OSD), each line was re-sequenced. DNA was extracted from flesh leaves of each strain and sequenced using NextSeq (Illumina). |