DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm

Abstract

DNA 6mA modification, an important newly discovered epigenetic mark, plays a crucial role in organisms and has been attracting more and more attention in recent years. The soybean is economically the most important bean in the world, providing vegetable protein for millions of people. However, the distribution pattern and function of 6mA in soybean are still unknown. In this study, we decoded 6mA modification to single-nucleotide resolution in wild and cultivated soybeans, and compared the 6mA differences between cytoplasmic and nuclear genomes and between wild and cultivated soybeans. The motif of 6mA in the nuclear genome was conserved across the two kinds of soybeans, and ANHGA was the most dominant motif in wild and cultivated soybeans. Genes with 6mA modification in the nucleus had higher expression than those without modification. Interestingly, 6mA distribution patterns in cytoplasm for each soybean were significantly different from those in nucleus, which was reported for the first time in soybean. Our research provides a new insight in the deep analysis of cytoplasmic genomic DNA modification in plants.

DNA adenine methylation in eukaryotes: Enzymatic mark or a form of DNA damage?

“…In animals and plants, 6mA levels are much higher in organellar than in nuclear DNA. [ 21,22 ] In animal mitochondria, the ratio of 6mA to A in DNA was estimated as roughly 400 ppm (parts per million). [ 21 ] For plant mitochondria, Vanyushin and colleagues reported an even higher figure of about 5000 ppm (=0.5%).…”

“…Comparative studies suggest that adenine methylation levels in plant chloroplasts are similar or even higher than in plant mitochondria. [ 22,24 ]…”

New Insights into Plant Extracellular DNA. A Study in Soybean Root Extracellular Trap

“…In mitochondrial DNA, only m6A is found, unlike plastids and nuclear DNA, which contain both of these types of methylation. Moreover, recently, m6A methylation density has been investigated in soybean, showing 1.4% for plastid DNA, 1.05% for mitochondrial DNA, and only 0.05% for nDNA [ 54 ]. Given this hypothesis, an exDNA methylation analysis might be done in order to understand if methylation processes are involved in the conservation of exDNA sequences.…”

Harnessing Current Knowledge of DNA N6-Methyladenosine From Model Plants for Non-model Crops

“…SMRT can detect every DNA modification at single base resolution ( Zhu et al, 2018 ). Recently, 6mA has been detected on genome-wide level in eudicot model Arabidopsis thaliana ( Liang et al, 2018b ) and monocot model rice ( Oryza sativa ) ( Zhang et al, 2018 ; Zhou et al, 2018 ), as well as in non-model plants Casuarina equisetifolia ( Ye et al, 2019 ), woodland strawberry ( Fragaria vesca ) ( Xie et al, 2020 ), and soyabeans ( Glycine max) ( Yuan et al, 2020 ), and fig ( Ficus carica ) ( Usai et al, 2021 ). While combined SMRT sequencing and 6mA-IP-Seq have been used to detect genome wide 6mA levels in Arabidopsis and rice ( Liang et al, 2018b ; Zhang et al, 2018 ; Zhou et al, 2018 ), and they reveals more efficient information for dynamic distribution and pattern of 6mA compared to these 6mA studies in non-model plants.…”

“…In Arabidopsis genome, 6mA is present in significant levels and broadly distributed with dynamic variation in its levels at different developmental stages in different tissues, which around 30% of 6mA exist on gene bodies ( Liang et al, 2018b ). Detected by SMRT-seq, a relatively abundant 6mA sites were located on gene bodies in other plants ( Zhang et al, 2018 ; Xie et al, 2020 ; Yuan et al, 2020 ). Within the gene bodies, about half of 6mA sites were located in exons (more than 80% in exons for Arabidopsis ) ( Figure 3A ).…”