N6-Methyladenine DNA Modification in the Woodland Strawberry (Fragaria vesca) Genome Reveals a Positive Relationship With Gene Transcription

Abstract

N 6 -methyladenine (6mA) DNA modification has been detected in several eukaryotic organisms, where it plays important roles in gene regulation and epigenetic memory maintenance. However, the genome-wide distribution patterns and potential functions of 6mA DNA modification in woodland strawberry (Fragaria vesca) remain largely unknown. Here, we examined the 6mA landscape in the F. vesca genome by adopting singlemolecule real-time sequencing technology and found that 6mA modification sites were broadly distributed across the woodland strawberry genome. The pattern of 6mA distribution in the long non-coding RNA was significantly different from that in proteincoding genes. The 6mA modification influenced the gene transcription and was positively associated with gene expression, which was validated by computational and experimental analyses. Our study provides new insights into the DNA methylation in F. vesca.

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 ).…”

“…Gene bodies include exons, introns, and 5′ and 3′ UTRs. Data were reproduced by previous studies ( Liang et al, 2018b ; Zhang et al, 2018 ; Xie et al, 2020 ; Yuan et al, 2020 ).…”

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

“…The raw sequencing reads in h5 format from the PacBio RSII platform (leaf) and the paired RNA-seq datasets (leaf and stem) of W05 ( Xie et al, 2019 ) were downloaded from the NCBI SRA database 1 , whereas the raw sequencing reads in h5 format from the sequel sequencing platform (leaf) and the paired RNA-seq datasets (leaf and stem) of ZH13 ( Shen et al, 2018 ) were downloaded from the Genome Sequence Archive (GSA) 2 . The accession numbers for all the downloaded datasets are listed in Table 1 .…”

“…The 4 bp upstream and downstream flanking each 6mA site were used to perform MEME-CHIP with default settings in order to predict the conservative motif of 6mA sites ( Ma et al, 2014 ; Liang et al, 2018 ; Zhang Q. et al, 2018 ; Li et al, 2020 ). According to the annotation of soybean genome, we divided the methylated nuclear gene regions into 5′ untranslated region (UTR), 3′ UTR, exons (exclude UTRs), and introns as described in literatures ( Liang et al, 2018 ; Zhang Q. et al, 2018 ; Xie et al, 2019 ). Similarly, the methylated cytoplasmic genes were separated into exons and introns according to the genome annotation in order to investigate 6mA distribution in gene features.…”