2015
DOI: 10.1186/s12870-015-0550-1
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Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic

Abstract: 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 a… Show more

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Cited by 30 publications
(31 citation statements)
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References 90 publications
(128 reference statements)
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“…Besides the localization in NORs, 5S rDNA locus, and telomeres the BAC-RAC1 also showed a disperse signals along the chromosomes giving a pattern already detected in other plant species (Santos et al, 2015 ). Here we report the first work evaluating by FISH the distribution of repetitive DNA elements in Eucalyptus , and it is in agreement with the distributition of LTR RTE detected in silico (Marcon et al, 2015 ) where RTEs subfamilies were identified dispersed along chromosomes arms in both gene-rich and repetitive-rich regions. The localization of BAC-RAC1 on subtelomeric domains in several chromosomes agrees with the identification of Copia RTEs near the telomeric regions (Marcon et al, 2015 ).…”
Section: Discussionsupporting
confidence: 90%
“…Besides the localization in NORs, 5S rDNA locus, and telomeres the BAC-RAC1 also showed a disperse signals along the chromosomes giving a pattern already detected in other plant species (Santos et al, 2015 ). Here we report the first work evaluating by FISH the distribution of repetitive DNA elements in Eucalyptus , and it is in agreement with the distributition of LTR RTE detected in silico (Marcon et al, 2015 ) where RTEs subfamilies were identified dispersed along chromosomes arms in both gene-rich and repetitive-rich regions. The localization of BAC-RAC1 on subtelomeric domains in several chromosomes agrees with the identification of Copia RTEs near the telomeric regions (Marcon et al, 2015 ).…”
Section: Discussionsupporting
confidence: 90%
“…A similar case happened during the annotation of transcriptionally active LTR-RTs in Eucalyptus (Marcon et al , 2015). An E. camaldulensis EST (GenBank accession FY783514), firstly identified because it contains a reverse transcriptase sequence, was in fact the fragment of a Caulimovirus .…”
Section: Introductionmentioning
confidence: 53%
“…In this way, having in mind that in silico analyses were based on the E. grandis genome, we used this species to run a comparative quantification of EgEVE_1 RVT domain by qPCR in E. urophylla, similar to the one performed by Marcon et al (2015), using a single-copy gene as a reference. Our analyses suggest that E. urophylla could have more EgEVE_1 copies than E. grandis (Figure 2).…”
Section: Resultsmentioning
confidence: 99%
“…Although the LTR-RTs are less likely to be actively expressed in plant tissues during normal development, several exceptions have been reported in various organs belonging to different species, such as Ogre elements in leaves, roots and flowers of pea [ 57 ], Grande elements in leaves of Zea and Tripsacum [ 58 ], eight LTR-RT families in leaves, stalks and roots of Eucalyptus genus [ 59 ], and EARE-1 elements in roots, staminate flowers, pistillate flowers, leaves and seeds of Excoecaria agallocha , which were all detected as transcriptionally active [ 60 ]. In our study, three families (12 AACA TEs) from pear were initially detected with transcriptional activity using the published RNA-seq data in the SRA database of NCBI, whereas no transcripts of the six families from peach ( PpTGTT1 ), mei ( PmTGTT1 and PmAACA1 ) and apple ( MdTGTT1 , MdTGTT2 and MdAACA1 ) were identified.…”
Section: Discussionmentioning
confidence: 99%