Identification of the post-transcriptional regulation reveals complexity in peanut pod development by Direct RNA

This study is led by Professor XiaoqinLiu (Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences, Shangdong, China). The authors explored post-transcriptional regulation, including polyadenylation, alternative splicing, and RNA adenosine methylation (m⁶A), in peanut pods across four developmental stages by performing direct RNA sequencing. A total of 14,627 newly identified transcripts and 6,769 new genes were generated from 12 samples at four developmental stages of peanut pods. These AS events were much more frequent at the AerPeg stage than at the three other stages, and most AS events representing only one type. However, a mutually exclusive exon type was always accompanied by other AS events.

There were obvious dynamic changes in the length of polyA at different stages of peanut pod development. The authors investigated the relationship between poly(A) length and transcript stability. The median poly(A) length for full_length reads was shorter than the median poly(A) length for non_full_length reads. Correlation analysis suggested a negative correlation between poly(A) length in transcripts and gene expression levels. In addition, an analysis of the relationship between variable AS and poly(A) length indicated that the poly(A) sequences in transcripts exhibiting alternative first exon, alternative last exon, exon skipping, and mutually exclusive exon were shorter than those of the other types. The splicing machinery utilized more proximal than distal alternative polyadenylation sites in the transcripts throughout pod development. The date showed no correlation between m⁶A modification and gene expression in peanut, however found more transcripts with alternative first and last exon types of alternative splicing events. The rate of m6A modification appeared to be lower in regions with higher proximal poly(A) levels compared with regions with higher distal poly(A) and unchanged poly(A) levels.

In summary, this work provides the first comprehensive analysis of post-transcriptional modifications during peanut pod development. The authors reveal the complex dynamics of post-transcriptional regulation during peanut pod development. The findings provide a new perspective for improving peanut cultivation through high yield breeding strategies and identification of new gene resources.

See the article:

Identification of the post-transcriptional regulation reveals complexity in peanut pod development by direct RNA

https://link.springer.com/article/10.1007/s42994-025-00224-5