A kingdom-wide full-length RNA atlas reveals the evolutionary landscapes of plant poly(A) tails

Abstract Background Poly(A) tails play crucial roles in regulating mRNA degradation and translation, yet their evolutionary dynamics remain largely unexplored. Results Here, we generate a comprehensive full-length RNA atlas of poly(A) tail based on 130 million nanopore long-read transcripts spanning major lineages from algae to angiosperms. We find lineage-specific tail-length profiles: most land plants display peaks at approximately 20 and 45 nt, whereas green algae show a distinct peak at approximately 40 nt. Unexpectedly, poly(A)-less histone mRNAs are detected in several plant lineages, but are independently lost multiple times and replaced by polyadenylated transcripts in Selaginella and all angiosperms. Across all species, terminal uridylation typically targets poly(A) tails shorter than 25 nt. Poly(A) tail lengths of whole genome duplication derived gene pairs diverge over time, yet certain genes maintain relatively conserved distributions across species, which underscores poly(A) length regulation as an important post-transcriptional regulatory layer. Conclusions Our study provides the first comprehensive poly(A) tail dataset spanning all major lineages of plant evolution, uncovering lineage-specific poly(A) tail length distributions. Notably, we reveal the presence of poly(A)-less transcripts in several plant clades, which is overlooked in previous transcriptomic studies. This atlas offers a valuable resource for understanding the evolutionary and regulatory complexity of mRNA 3′ end formation across the plant kingdom.