English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

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.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-615) contains supplementary material, which is available to authorized users.

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