Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes
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.
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Biblioteca del CIRAD Francia |
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F30 - Génétique et amélioration des plantes Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes Transcription génique génome mécanisme de défense stress dû à la sécheresse séquence d'arn résistance à la sécheresse génie génétique stress abiotique stress biotique http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_35269 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_27813 http://aims.fao.org/aos/agrovoc/c_2392 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35768 http://aims.fao.org/aos/agrovoc/c_35769 http://aims.fao.org/aos/agrovoc/c_1070 F30 - Génétique et amélioration des plantes Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes Transcription génique génome mécanisme de défense stress dû à la sécheresse séquence d'arn résistance à la sécheresse génie génétique stress abiotique stress biotique http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_35269 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_27813 http://aims.fao.org/aos/agrovoc/c_2392 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35768 http://aims.fao.org/aos/agrovoc/c_35769 http://aims.fao.org/aos/agrovoc/c_1070 |
spellingShingle |
F30 - Génétique et amélioration des plantes Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes Transcription génique génome mécanisme de défense stress dû à la sécheresse séquence d'arn résistance à la sécheresse génie génétique stress abiotique stress biotique http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_35269 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_27813 http://aims.fao.org/aos/agrovoc/c_2392 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35768 http://aims.fao.org/aos/agrovoc/c_35769 http://aims.fao.org/aos/agrovoc/c_1070 F30 - Génétique et amélioration des plantes Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes Transcription génique génome mécanisme de défense stress dû à la sécheresse séquence d'arn résistance à la sécheresse génie génétique stress abiotique stress biotique http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_35269 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_27813 http://aims.fao.org/aos/agrovoc/c_2392 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35768 http://aims.fao.org/aos/agrovoc/c_35769 http://aims.fao.org/aos/agrovoc/c_1070 Lopes, Fabrício R. Jjingo, Daudi Da Silva, Carlos R.M. Andrade, Alan Carvalho Marraccini, Pierre Teixeira, João B. Carazzolle, Marcelo Falsarella Pereira, Gonçalo Amarante Guimarães Pereira, Luiz Filipe P. Vanzela, André L.L. Wang, Lu Jordan, King Carareto, Claudia M.A. Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes Transcription génique génome mécanisme de défense stress dû à la sécheresse séquence d'arn résistance à la sécheresse génie génétique stress abiotique stress biotique http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_35269 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_27813 http://aims.fao.org/aos/agrovoc/c_2392 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35768 http://aims.fao.org/aos/agrovoc/c_35769 http://aims.fao.org/aos/agrovoc/c_1070 |
author |
Lopes, Fabrício R. Jjingo, Daudi Da Silva, Carlos R.M. Andrade, Alan Carvalho Marraccini, Pierre Teixeira, João B. Carazzolle, Marcelo Falsarella Pereira, Gonçalo Amarante Guimarães Pereira, Luiz Filipe P. Vanzela, André L.L. Wang, Lu Jordan, King Carareto, Claudia M.A. |
author_facet |
Lopes, Fabrício R. Jjingo, Daudi Da Silva, Carlos R.M. Andrade, Alan Carvalho Marraccini, Pierre Teixeira, João B. Carazzolle, Marcelo Falsarella Pereira, Gonçalo Amarante Guimarães Pereira, Luiz Filipe P. Vanzela, André L.L. Wang, Lu Jordan, King Carareto, Claudia M.A. |
author_sort |
Lopes, Fabrício R. |
title |
Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes |
title_short |
Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes |
title_full |
Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes |
title_fullStr |
Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes |
title_full_unstemmed |
Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes |
title_sort |
transcriptional activity, chromosomal distribution and expression effects of transposable elements in coffea genomes |
url |
http://agritrop.cirad.fr/571220/ http://agritrop.cirad.fr/571220/1/document_571220.pdf |
work_keys_str_mv |
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1792498549630435328 |
spelling |
dig-cirad-fr-5712202024-01-28T21:43:20Z http://agritrop.cirad.fr/571220/ http://agritrop.cirad.fr/571220/ Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes. Lopes Fabrício R., Jjingo Daudi, Da Silva Carlos R.M., Andrade Alan Carvalho, Marraccini Pierre, Teixeira João B., Carazzolle Marcelo Falsarella, Pereira Gonçalo Amarante Guimarães, Pereira Luiz Filipe P., Vanzela André L.L., Wang Lu, Jordan King, Carareto Claudia M.A.. 2013. PloS One, 8 (11):e78931, 16 p.https://doi.org/10.1371/journal.pone.0078931 <https://doi.org/10.1371/journal.pone.0078931> Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes Lopes, Fabrício R. Jjingo, Daudi Da Silva, Carlos R.M. Andrade, Alan Carvalho Marraccini, Pierre Teixeira, João B. Carazzolle, Marcelo Falsarella Pereira, Gonçalo Amarante Guimarães Pereira, Luiz Filipe P. Vanzela, André L.L. Wang, Lu Jordan, King Carareto, Claudia M.A. eng 2013 PloS One F30 - Génétique et amélioration des plantes Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes Transcription génique génome mécanisme de défense stress dû à la sécheresse séquence d'arn résistance à la sécheresse génie génétique stress abiotique stress biotique http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_35128 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_35269 http://aims.fao.org/aos/agrovoc/c_24993 http://aims.fao.org/aos/agrovoc/c_27813 http://aims.fao.org/aos/agrovoc/c_2392 http://aims.fao.org/aos/agrovoc/c_15974 http://aims.fao.org/aos/agrovoc/c_35768 http://aims.fao.org/aos/agrovoc/c_35769 Brésil http://aims.fao.org/aos/agrovoc/c_1070 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/571220/1/document_571220.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1371/journal.pone.0078931 10.1371/journal.pone.0078931 info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0078931 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1371/journal.pone.0078931 |