Bisulfite-Seq and RNA-seq profiling of Arabidopsis aneuploids

Aneuploidy refers to gains and/or losses of individual chromosomes from the normal chromosome set. The resulting gene dosage imbalance usually has a deleterious effect on the phenotype, as illustrated in humans by Down Syndrome (trisomy 21) and solid tumor cells, which are typically highly aneuploid. Aneuploidy has been studied for many years in plants and has been a factor contributing to plant chromosome evolution. Nevertheless, there is still relatively little information about how chromosome numerical imbalances affect the molecular constitution of cells and confer altered phenotypes. To investigate these questions we have performed comparative transcriptome (RNA-seq) and methylome (bisulfite-seq) analyses on trisomics (2n+1) of all five chromosomes of Arabidopsis thaliana as well as matched diploids, triploid and tetraploids. Overall design: Trisomics of each of the five Arabidopsis thaliana chromosomes were screened out microscopically at the seedling stage from a population of selfed progeny of a triploid parent using fluorescent-tags on specific chromosomes as markers. The triploid parents are obtained as progeny from a cross between a diploid and a tetraploid. The trisomics were grown in soil and the number of chromosomes was confirmed by counting metaphase chromosomes prepared from flower pistils and by comparative genome hybridization. At least two biological replicates representing each confirmed karyotype (trisomies 1 through 5, diploid, triploid, tetraploid) were used for DNA and RNA isolation. DNA and RNA preparations as well as RNA-seq and bisulfite-seq were carried out according to standard procedures.