Comparison of AP13 and VS16 Switchgrass (Panicum virgatum) Methylomes Using High-Throughput Sequencing

Switchgrass (Panicum virgatum) is a target crop, which possesses several appealing qualities for use as a bioenergy feedstock for ethanol production. Switchgrass has high biomass yield from low nutrient input, high water use efficiency, and broad adaptability. There are two major ecotypes of switchgrass which are lowland and upland. Lowland ecotypes are typically tetraploids that originated in the southern east coastal region and upland ecotypes are usually octoploid which originated in northern regions of the U.S. Both the AP13 (lowland) VS16 (upland) are tetraploid (2n = 4x = 36). Currently, the publicly available genome sequence is assembled from AP13 in 18 scaffolds (Phytozome V1.1). In these scaffolds 636 Mb of sequence has been localized, with another 596.5 Mb of sequence that is arranged in contigs (~1,230 Mb).  

Genome annotation and assembly are critical in providing resources for selection and breeding of biotic and abiotic stress-resistant plants. Response to stresses is correlated with changes in gene expression, which is regulated by transcription factors and also epigenetic factors. This study focused on one epigenetic factor, called DNA methylation, which is the addition of a methyl group on the 5’ carbon of cytosines. Genome-wide methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) and whole genome bisulfite-sequencing (BS-Seq) was performed to compare methylation levels between the two genotypes. MeDIP-Seq surveys overall differences between the genomes and BS-Seq gives specific methylation statuses of individual cytosines. We found that AP13 had 4,667 more MeDIP-Seq peaks than VS16 (21,287 peaks). Average promoter and genic methylation was highest in the CG context.