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 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.

Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes

“…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 ).…”

Genome-wide analysis of EgEVE_1, a transcriptionally active endogenous viral element associated to small RNAs in Eucalyptus genomes

“…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 .…”

“…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).…”

TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species

“…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.…”