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



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.



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.
Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil. helenasmarcon@gmail.com.|Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil. helenasmarcon@gmail.com.
Helena Sanches
HS
Marcon
Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil. doug@rc.unesp.br.|Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil. doug@rc.unesp.br.
Douglas Silva
DS
Domingues
Plant Biotechnology Laboratory, Instituto Agronômico do Paraná - IAPAR, Londrina, Brazil. julianacostasilvati@gmail.com.
Juliana Costa
JC
Silva
Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil. rafaeljborges@hotmail.com.|Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil. rafaeljborges@hotmail.com.
Rafael Junqueira
RJ
Borges
Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil. fabiofima@ibb.unesp.br.
Fábio Filippi
FF
Matioli
Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil. fontes@ibb.unesp.br.|Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil and INCTTOX-CNPq, Brazil. fontes@ibb.unesp.br.
Marcos Roberto de Mattos
MR
Fontes
Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, Brazil. clmarino@ibb.unesp.br.|Programa de Pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista - UNESP, Botucatu, Brazil. clmarino@ibb.unesp.br.|Instituto de Biotecnologia da UNESP - IBTEC, Botucatu, Brazil. clmarino@ibb.unesp.br.
Celso Luis
CL
Marino
D005052:Eucalyptus / Q000235:genetics* / Q000378:metabolism; D018745:Genome, Plant; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D017433:Protein Structure, Secondary; D018626:Retroelements; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences; D059467:Transcriptome
D010940:Plant Proteins; D018626:Retroelements