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

Xiaohui Wu, Bobby Gaffney, Arthur G. Hunt, Qingshun Q. Li

Research output: Contribution to journalArticlepeer-review

25 Scopus citations

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.

Original languageEnglish
Article number615
JournalBMC Genomics
Volume15
Issue number1
DOIs
StatePublished - Jul 21 2014

Bibliographical note

Funding Information:
This work was supported by a grant from US National Science Foundation [IOS-0817818; to QQL and AGH], and a grant from Ohio Plant Biotech Consortium to QQL. Additional funding supports were also from Xiamen University and The 100-Talent Plan of Fujian Province, China. This project was also funded by the National Natural Science Foundation of China (Nos. 61201358, 61174161), the Natural Science Foundation of Fujian Province of China (No. 2012J01154), and the specialized Research Fund for the Doctoral Program of Higher Education of China (Nos. 20100121120022 and 20120121120038), and the Fundamental Research Funds for the Central Universities in China (Xiamen University: No. 2013121025).

Keywords

  • Alternative polyadenylation
  • Antisense
  • Evolutionary conservation
  • Legume
  • Medicago truncatula
  • RNA processing

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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