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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Lopes, Fabricio R. [1] ; Jjingo, Daudi [2] ; da Silva, Carlos R. M. [3] ; Andrade, Alan C. [4] ; Marraccini, Pierre [4, 5] ; Teixeira, Joao B. [4] ; Carazzolle, Marcelo F. [6] ; Pereira, Goncalo A. G. [6] ; Pereira, Luiz Filipe P. [7] ; Vanzela, Andre L. L. [3] ; Wang, Lu [2] ; King Jordan, I. [2, 8] ; Carareto, Claudia M. A. [1]
Total Authors: 13
[1] Univ Estadual Paulista, Univ Estadual Paulista Julio de Mesquita Filho, Dept Biol, Sao Jose do Rio Preto - Brazil
[2] Georgia Inst Technol, Sch Biol, Atlanta, GA 30332 - USA
[3] Univ Estadual Londrina, Dept Biol Geral, Londrina - Brazil
[4] Empresa Brasileira Pesquisa Agr Recursos Genet &, Brasilia, DF - Brazil
[5] Ctr Cooperat Int Rech Agron Dev, UMR AGAP, Montpellier - France
[6] Univ Estadual Campinas, Dept Genet Evolucao & Bioagentes, Campinas, SP - Brazil
[7] Empresa Brasileira Pesquisa Agr Cafe, Brasilia, DF - Brazil
[8] PanAmer Bioinformat Inst, Santa Marta, Magdalena - Colombia
Total Affiliations: 8
Document type: Journal article
Source: PLoS One; v. 8, n. 11 NOV 11 2013.
Web of Science Citations: 12

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. (AU)

FAPESP's process: 08/05894-1 - Expression analysis of genes harboring cassetes and active tes in diploid (c. canephora, c. eugenoides, c. racemosa) and poliploid (c. arabica) Coffea species
Grantee:Claudia Marcia Aparecida Carareto
Support type: Regular Research Grants