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Open Access Research article

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

Xiaohui Wu1, Bobby Gaffney2, Arthur G Hunt2* and Qingshun Q Li345*

Author Affiliations

1 Department of Automation, Xiamen University, Xiamen, China

2 Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA

3 Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China

4 Department of Biology, Miami University, Oxford, OH, USA

5 Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian, China

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BMC Genomics 2014, 15:615  doi:10.1186/1471-2164-15-615

Published: 21 July 2014

Abstract

Background

Alternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of gene expression. Little is known about how APA sites may evolve in homologous genes in different plant species. To this end, comparative studies of APA sites in different organisms are needed. In this study, a collection of poly(A) sites in Medicago truncatula, a model system for legume plants, has been generated and compared with APA sites in Arabidopsis thaliana.

Results

The poly(A) tags from a deep-sequencing protocol were mapped to the annotated M. truncatula genome, and the identified poly(A) sites used to update the annotations of 14,203 genes. The results show that 64% of M. truncatula genes possess more than one poly(A) site, comparable to the percentages reported for Arabidopsis and rice. In addition, the poly(A) signals associated with M. truncatula genes were similar to those seen in Arabidopsis and other plants. The 3′-UTR lengths are correlated in pairs of orthologous genes between M. truncatula and Arabidopsis. Very little conservation of intronic poly(A) sites was found between Arabidopsis and M. truncatula, which suggests that such sites are likely to be species-specific in plants. In contrast, there is a greater conservation of CDS-localized poly(A) sites in these two species. A sizeable number of M. truncatula antisense poly(A) sites were found. A high percentage of the associated target genes possess Arabidopsis orthologs that are also associated with antisense sites. This is suggestive of important roles for antisense regulation of these target genes.

Conclusions

Our results reveal some distinct patterns of sense and antisense poly(A) sites in Arabidopsis and M. truncatula. In so doing, this study lends insight into general evolutionary trends of alternative polyadenylation in plants.

Keywords:
Alternative polyadenylation; RNA processing; Antisense; Evolutionary conservation; Legume; Medicago truncatula