Genome-wide determination of poly(A) sites in medicago truncatula: Evolutionary conservation of alternative poly(A) site choice

Polyadenylation is a critical process during gene expression in eukaryotic cells, and plays important roles in mRNA stability, translation, and transport. Genes with more than one poly(A) site are able to produce mRNAs encoding different protein products or mRNAs with different 3′ UTRs through alternative polyadenylation (APA). To systematically investigate APA in plants, a 3′ end sequencing protocol was adopted to obtain transcriptome‐wide poly(A) sites in Medicago truncatula. Similar to the extent found in Arabidopsis thaliana and rice, up to 64% of M. truncatula genes possess APA sites. Comparative studies of APA sites between M. truncatula and A. thaliana were conducted to gain insight into general evolutionary trends of APA in plants. The length of the 3′ UTRs of pairs of orthologous genes between M. truncatula and A. thaliana was correlated. Poly(A) signals and nucleotide compositions of sequence around poly(A) sites are conserved in the plant kingdom. The conservation of poly(A) sites in coding regions was higher than that of intronic poly(A) sites between A. thaliana and M. truncatula. These results reveal the evolutionary conservation of the plant APA. APA has been reported to be essential for the expression of a nodule‐specific membrane protein. An open‐access web service called PlantAPA (http://bmi.xmu.edu.cn/plantapa/) was also built to retrieve, query, visualize, and analyze genome‐wide poly(A) sites in plants including rice, A. thaliana, M. truncatula, and Chlamydomonas reinhardtii.