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

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dc.contributor.authorLopes, Fabrício R.
dc.contributor.authorJjingo, Daudi
dc.contributor.authorR. M. da Silva, Carlos
dc.contributor.authorAndrade, Alan C.
dc.contributor.authorMarraccini, Pierre
dc.contributor.authorTeixeira, Joaõ B.
dc.contributor.authorCarazzolle, Marcelo F.
dc.contributor.authorA. G. Pereira, Gonçalo
dc.contributor.authorPereira, Luiz Filipe P.
dc.contributor.authorVanzela, André L. L.
dc.contributor.authorWang, Lu
dc.contributor.authorJordan, I. King
dc.contributor.authorCarareto, Claudia M. A.
dc.date.accessioned2018-12-17T15:04:55Z
dc.date.accessioned2021-12-21T08:58:56Z
dc.date.available2018-12-17T15:04:55Z
dc.date.available2021-12-21T08:58:56Z
dc.date.issued2013-11-11
dc.descriptionThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_US
dc.description.abstractPlant 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.en_US
dc.description.sponsorshipThis study was funded by grants provided by the Brazilian agencies Fundac¸a˜o de Amparo a` Pesquisa do Estado de Sa˜o Paulo (2008/05894-1 to CMAC and fellowship 2007/55985-0 to FRL) and Conselho Nacional de Desenvolvimento Cientı´fico e Tecnolo´ gico (to CMAC). The authors thank the Centre de Coope´ration Internationale en Recherche Agronomique pour le De´veloppement for the grant (ATP project ‘‘Plasticite´ phe´notypique des pe´rennes sous contrainte hydrique au champ’’ to PM and ACA) that permitted the study of C. arabica cultivars. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en_US
dc.identifier.citationLopes FR, Jjingo D, da Silva CRM, Andrade AC, Marraccini P, et al. (2013). Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes. PLoS ONE 8(11): e78931. doi:10.1371/journal.pone.0078931en_US
dc.identifier.urihttps://hdl.handle.net/20.500.11951/643
dc.language.isoenen_US
dc.publisherPLoS ONE (Public Library of Science)en_US
dc.subjectTransposable elements (TE), Plant genomes - Coffea canephoraen_US
dc.subjectTransposable elements (TE), Plant genomes - Coffea eugenioidesen_US
dc.subjectTransposable elements (TE), Plant genomes - Coffea arabicaen_US
dc.subjectCofea - plant genomes (Transposable elements)en_US
dc.titleTranscriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomesen_US
dc.typeArticleen_US
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