Genome-Wide DNA Methylation Profiling in the Lotus (Nelumbo nucifera) Flower Showing its Contribution to the Stamen Petaloid.

Zhongyuan Lin,Kefang Ou,Rebecca Njeri Damaris,Meihui Liu,Tonny Maraga Nyong’A,Dingding Cao,Pingfang Yang

doi:10.3390/plants8050135

Abstract

DNA methylation is a vital epigenetic modification. Methylation has a significant effect on the gene expression influencing the regulation of different physiological processes. Current studies on DNA methylation have been conducted on model plants. Lotus (Nelumbo nucifera) is a basic eudicot exhibiting variations during development, especially in flower formation. DNA methylation profiling was conducted on different flower tissues of lotuses through whole genome bisulfite sequencing (WGBS) to investigate the effects of DNA methylation on its stamen petaloid. A map of methylated cytosines at the single base pair resolution for the lotus was constructed. When the stamen was compared with the stamen petaloid, the DNA methylation exhibited a global decrease. Genome-wide relationship analysis between DNA methylation and gene expression identified 31 different methylation region (DMR)-associated genes, which might play crucial roles in floral organ formation, especially in the stamen petaloid. One out of 31 DMR-associated genes, NNU_05638 was homolog with Plant U-box 33 (PUB33). The DNA methylation status of NNU_05638 promoter was distinct in three floral organs, which was confirmed by traditional bisulfite sequencing. These results provide further insights about the regulation of stamen petaloids at the epigenetic level in lotus.

Highlights

DNA methylation is one of the vital features of epigenetic modification, which plays a key role in plant growth and development through its regulation of gene expression [1,2,3]
Our results indicate that the stamen petaloid is derived from the stamen and similar to a petal
The profile of DNA methylation in these three lotus organs suggests that the effects of DNA methylation were located in the stamen petaloid

Summary

Introduction

DNA methylation is one of the vital features of epigenetic modification, which plays a key role in plant growth and development through its regulation of gene expression [1,2,3]. DNA methylation occurs in all cytosine sequence contexts including CG and non-CG (CHG and CHH, where H represents any nucleotide but G) in plant genomes [4]. These three sequence contexts are maintained by individual enzymatic pathways [5]. CG methylation is maintained by methyltransferase 1 (MET1), the plant homolog of DNA methyltransferase 1 (DNMT1) in animals [6]. DNA methylation in CHG and CHH is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM)

Methods

Results

Conclusion