Analysis of Polyadenylation Signal Usage with Full-Length Transcriptome in Spodoptera frugiperda (Lepidoptera: Noctuidae)

SIMPLE SUMMARY: RNA polyadenylation is an important process in mRNA maturation. The process is controlled by various cis-acting elements surrounding the cleavage site, and their binding factors. Recently high sequencing technology especially full-length transcriptome provides a large amount of sequencing data for us to explore the variations of poly(A) signals, alternative polyadenylation (APA) in Spodoptera frugiperda. We studied 50,616 polyadenylation signals using full-length transcriptome and EST data. These data show that 51.64% of the 50,616 pA sites had the conserved AAUAAA hexamers, while 10.13% of pA sites had none of the AAUAAA-like hexamers. Among these genes, more than 64.76% have more than one pA site. Our results also support that APA plays a significant role in increasing transcriptome diversity and gene expression regulation in Spodoptera frugiperda. Our dataset was the first polyadenylation signal analysis in the Lepidoptera and would provide a theoretical basis for pest control. ABSTRACT: During the messenger RNA (mRNA) maturation process, RNA polyadenylation is a key step, and is coupled to the termination of transcription. Various cis-acting elements near the cleavage site and their binding factors would affect the process of polyadenylation, and AAUAAA, a highly conserved hexamer, was the most important polyadenylation signal (PAS). PAS usage is one of the critical modification determinants targeted at mRNA post-transcription. The full-length transcriptome has recently generated a massive amount of sequencing data, revealing poly(A) variation and alternative polyadenylation (APA) in Spodoptera frugiperda. We identified 50,616 polyadenylation signals in Spodoptera frugiperda via analysis of full-length transcriptome combined with expression Sequence Tags Technology (EST). The polyadenylation signal usage in Spodoptera frugiperda is conserved, and it is similar to that of flies and other animals. AAUAAA and AUUAAA are the most highly conserved polyadenylation signals of all polyadenylation signals we identified. Additionally, we found the U/GU-rich downstream sequence element (DSE) in the cleavage site. These results demonstrate that APA in Spodoptera frugiperda plays a significant role in root growth and development. This is the first polyadenylation signal usage analysis in agricultural pests, which can deepen our understanding of Spodoptera frugiperda and provide a theoretical basis for pest control.