Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.).

Wenqiu Lin,Weisheng Sun,Xi’ou Xiao,Xiumei Zhang,Yunhe Li,Hongna Zhang,Qingsong Wu,Shenghui Liu

doi:10.3390/genes10110877

Abstract

DNA methylation changes can occur in some loci during callus culture, resulting in somaclonal variations (SVs). In the present study, we applied whole genome bisulfite sequencing to analyze context-specific DNA methylation changes in the pineapple genome between the cutting seedings and 5 SV plants. In general, SV plants exhibited methylation patterns analogous to those of cutting seedlings (CK). A total of 27.98% of the genomic cytosines of CK were methylcytosines, which was higher than that of 5 SV plants. Moreover, mCG and mCHG was hypermethylated, whereas mCHH was hypomethylated among the 5 SV plants genomic when compared with the CK. Most of the variation of DNA methylation was distributed in gene bodies, thus suggesting that phenotypic differences are probably perturbed by genes methylated from callus culture. In addition, the methylated genes were highly enriched for the Gene Ontology (GO) categories of binding and catalytic activity, cell part and organelle, cellular process, abiotic stimulus, and DNA modification. These results suggest that methylation mediates these pathways in the callus culture of pineapple. The results also suggested that the callus culture induced DNA methylation may result in the SV.

Highlights

DNA methylation is an epigenetic modification that plays a critical role in diverse biological processes, including regulation of gene expression [1], cellular differentiation [2], development [3], and stress responses [4]
The clean reads were mapped to sequences that are unique in the genome after bisulfite conversion from every possible methylation pattern, and the mapping rates ranged from 83.31% to 86.03% (Table S1)
The coverage rate of CG ranged from 79.19% to 82.71%, and the CHG ranged from 81.94% to 83.35%, while CHH

Summary

Introduction

DNA methylation is an epigenetic modification that plays a critical role in diverse biological processes, including regulation of gene expression [1], cellular differentiation [2], development [3], and stress responses [4]. DNA methylation is categorized in terms of site classes as CG, CHG, or CHH (H = A, C, or T) based on the sequence context accompanied by the methylated C (mC). According to enrichment tests for each site class, at least five classes of methylated genes, including unmethylated, gene body methylated, transcriptional start, CG/CHG genes, and CHH/RdDM genes, have been determined [5]. The methylated gene body is evolutionary conserved, while the transcriptional start. CG/CHG and CHH/RdDM genes are not conserved. In-vitro culture induces somaclonal variations (SVs) in plants [6]. DNA methylation/demethylation is affected by in-vitro propagation, which comprises a dedifferentiation (callus formation) process followed by a re-differentiation (plant regeneration) course [11].

Methods

Results

Conclusion