Comparison of Methylome Sequencing Using MeDIP-Seq and Sodium Bisulfite Sequencing in Common Bean (Phaseolus vulgaris)

Common bean (Phaseolus vulgaris) is the most widely consumed legume, as it is high in protein, fiber, and essential nutrients. Common bean has a relatively small diploid genome, consisting of about 587 megabases. This species is comprised of variable sizes and colors of beans including navy, black, great northern, pinto, kidney beans and more. Biotic and abiotic stresses can cause extreme bean yield loss. For example, Uromyces appendiculatus, known as bean rust, is reported to cause yield losses from 18-100%. Stress-induced DNA methylation occurs in genes that are stress-related, but also at random.

DNA methylation is an epigenetic modification, which plays a significant role in gene expression; therefore, it is essential for tissue specialization and transposon inactivation. In plants, cytosine methylation occurs mainly in the CG dinucleotide sequence, but also on cytosines in the CHG or CHH contexts. Methylated regions in the contexts of CHG and CG are symmetrical; therefore, are conserved during DNA replication, while CHH is generated by de novo methylation. In comparison to animals, plants tend to exhibit more DNA methylation that is inherited by the offspring. This is partially attributed to the difference in germline development. 

There are several methods for determining the presence and location of methylated cytosines in the genome; including, methylation-sensitive restriction enzyme sequencing, affinity purification, and bisulfite sequencing. Whole genome bisulfite sequencing (WGBS) is accepted as the “gold standard” of methyl sequencing. This study compares whole genome bisulfite sequencing and methylated DNA immunoprecipitation sequencing of the Phaseolus vulgaris methylome.