Identification and frequency of transposable elements in Eucalyptus

Bacci, Maurício; Soares, Rafael B.S.; Tajara, Eloíza H.; Ambar, Guilherme; Fischer, Carlos Norberto; Guilherme, Ivan Rizzo; Costa, Eduardo Paulino da; Miranda, Vitor F. O.

doi:10.1590/s1415-47572005000400019

Cited by 5 publications

(4 citation statements)

References 25 publications

(26 reference statements)

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“…In Saccharum officinarum , out of 260,781 ESTs, 276 (0.1%) were considered to be expressed TEs [38] . Finally, in Eucalyptus grandis , out of 123,889 ESTs, 124 (0.1%) were identified as transcriptionally active TEs [39] . Our data reinforce the fact that TEs are poorly represented in the Coffea transcriptome, although plant genomes are enriched by those repetitive sequences.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2013

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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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Section: Discussionmentioning

confidence: 99%

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

et al. 2013

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“…Up to now, TE dynamics were scarcely studied in the Eucalyptus genus and most analysis were based on private EST data [i.e. [ 14 ]. In the present study, we identify and comprehensively characterize a selected group of Eucalyptus LTR-RTEs, emphasizing the characterization of elements with putative transcriptional activity.…”

Section: Introductionmentioning

confidence: 99%

Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic

et al. 2015

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BackgroundIn Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome.ResultsWe characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one Copia family, RLC_egBianca_1. Protein theoretical models suggest different properties between Copia and Gypsy domains. IRAP and REMAP markers suggested genomic polymorphisms among Eucalyptus species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values.ConclusionOur strategy was successful in isolating transcriptionally active retrotransposons in Eucalyptus, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among Eucalyptus species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0550-1) contains supplementary material, which is available to authorized users.

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“…Over the last 10 years, an abundance of experimental evidence has accumulated that directly points to the contribution of transposable elements (TEs) to host gene structure, function and expression (Britten, 1996a(Britten, ,b, 1997(Britten, , 2004Nekrutenko and Li, 2001;Landry et al, 2001Landry et al, , 2002Landry and Mager, 2003;Sorek et al, 2002;Jordan et al, 2003;Lorenc and Makalowski, 2003; Van de Lagemaat et al, 2003;Jordan et al, 2003;Boeke, 2004, 2005;Bacci et al, 2005;Dunn et al, 2005Dunn et al, , 2006DeBarry et al, 2005;Ganko et al, 2003;Ganko, 2006). These studies also have shown that the evolutionary consequences of TE insertions in the host genome are diverse when they occur within genes.…”

Section: Introductionmentioning

confidence: 99%