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

Background: In 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. Results: We
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. Conclusion:
Our 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.