Dataset Information

Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

ABSTRACT:

Background

Cucumber green mottle mosaic virus (CGMMV) causes substantial global losses in cucurbit crops, especially watermelon. N6-methyladenosine (m6A) methylation in RNA is one of the most important post-transcriptional modification mechanisms in eukaryotes. It has been shown to have important regulatory functions in some model plants, but there has been no research regarding m6A modifications in watermelon.

Results

We measured the global m6A level in resistant watermelon after CGMMV infection using a colorimetric method. And the results found that the global m6A level significantly decreased in resistant watermelon after CGMMV infection. Specifically, m6A libraries were constructed for the resistant watermelon leaves collected 48 h after CGMMV infection and the whole-genome m6A-seq were carried out. Numerous m6A modified peaks were identified from CGMMV-infected and control (uninfected) samples. The modification distributions and motifs of these m6A peaks were highly conserved in watermelon transcripts but the modification was more abundant than in other reported crop plants. In early response to CGMMV infection, 422 differentially methylated genes (DMGs) were identified, most of which were hypomethylated, and probably associated with the increased expression of watermelon m6A demethylase gene ClALKBH4B. Gene Ontology (GO) analysis indicated quite a few DMGs were involved in RNA biology and stress responsive pathways. Combined with RNA-seq analysis, there was generally a negative correlation between m6A RNA methylation and transcript level in the watermelon transcriptome. Both the m6A methylation and transcript levels of 59 modified genes significantly changed in response to CGMMV infection and some were involved in plant immunity.

Conclusions

Our study represents the first comprehensive characterization of m6A patterns in the watermelon transcriptome and helps to clarify the roles and regulatory mechanisms of m6A modification in watermelon in early responses to CGMMV.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12870-021-03289-8.

SUBMITTER: He Y

PROVIDER: S-EPMC8574010 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:In mammals, skeletal muscle development is a complex biological process regulated by many factors. N6-methyladenosine (m6A) RNA modification plays an important role in many biological processes. However, the regulation of m6A on skeletal muscle growth and development in adult goats remains unclear. In this study, Duan goats (DA) and Nubia goats (NBY), both female and 12 months old, were selected as the research objects, and m6A-Seq and RNA-Seq were mainly used to detect the difference of m6A modification and gene expression during the development of the longissimus dorsi (LD) muscle in the two breeds. The results showed that compared with DA, the meat production performance of NBY was better than that of DA, and the modification level of m6A was higher than that of DA in LD. The m6A-Seq of LD indicated m6A peaks were mainly enriched in the coding sequence (CDS) and stop codon. A total of 161 differentially methylated genes (DMGs) and 1294 differentially expressed genes (DEGs) were identified in two breeds. GO and KEGG analysis showed that DMGs were closely related to cellular metabolism, and most of DMGs were enriched in pathways related to energy metabolism, muscle growth and development, mainly MAPK signaling pathway, Wnt signaling pathway and CGMP-PKG signaling pathway. The DEGs were significantly enriched in actin binding, calcium ion binding, angiogenesis, and other biological processes, and most of them were enriched in PI3K-Akt and CGMP-PKG signaling pathways. Combined analysis of m6A-Seq and RNA-Seq data revealed a negative correlation between differentially methylated m6A levels and mRNA abundance, and mRNA expression of the gene with m6A peak near 3'UTR will decrease. In addition, 11 DMGs regulating cell differentiation, muscle growth and development were identified. This study displayed the m6A profiles and distribution patterns in the goat transcriptome, determined the potential role of m6A modification in muscle growth and provided a new reference for the further study of goat skeletal muscle development.