Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

Fabrício R Lopes,Claudia M A Carareto,João B Teixeira,Luiz Filipe P Pereira,Alan C Andrade,Daudi Jjingo,Pierre Marraccini,Gonçalo A G Pereira,I King Jordan,Marcelo F Carazzolle,Lu Wang,André L L Vanzela,Carlos R M Da Silva

doi:10.1371/journal.pone.0078931

Fabrício R Lopes, Claudia M A Carareto + Show 11 more

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https://doi.org/10.1371/journal.pone.0078931

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Abstract

Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences.

Highlights

Transposable elements (TEs) are genetic entities with an intrinsic mobilization capacity
This study provides a preliminary understanding of the TE regulatory dynamics in the allotetraploid and complex genome of C. arabica
The findings presented here show that this species is an interesting study organism because most DNA transposons and retrotransposons seem to be submitted to fine transcriptional control

Summary

Introduction

Transposable elements (TEs) are genetic entities with an intrinsic mobilization capacity. As a result of this characteristic, they are responsible for donating regulatory sequences [1] and transcription regulatory signals [2], as well as for creating considerable genomic instability, mediating chromosome rearrangements [3], altering both gene expression and function [1], and creating novel genes and exons [4]. Such mobilization can result in host genome contraction and expansion [5], [6]. Class II (DNA transposons) elements are split into two subclasses: subclass I contains superfamilies either with terminal inverted repeats (Tc1-Mariner, hAT, Mutator, Merlin, Transib, P, PiggyBac, PIF-Harbinger and Cacta) or without terminal inverted repeats (Crypton), whereas subclass II comprises the Helitron and Maverick superfamilies

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