Characterization of Three Novel Gypsy-like Retrotransposon Families in Eucalyptus Genome

LTR Retrotransposons (RTEs) represent the most abundant and dynamic fraction of genomes in most plant species. They are usually divided in two main superfamilies: Copia and Gypsy. In this work, we used an in silico approach to identify transcriptionally active Gypsy-like RTEs in Eucalyptus genus. We identified three retrotransposon families, belonging to different evolutive lineages: Athila, Tat and Tekay. The families are between 4.4 and 18.3 kb.  BLAT analysis in Eucalyptus grandis draft genome identified that these elements are between 23 and 93 copies. Inter-retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP) of these elements were accessed in five eucalyptus species, to provide information on genetic diversity: E. brassiana, E. grandis, E. saligna, E. tereticornis and E. urophylla.  Five IRAP primers generated 494 fragments (98.4 fragments/primer) displaying 92 polymorphic fragments. Eight REMAP primer combinations produced 313 fragments with 145 polymorphic bands. E. grandis and E. saligna were the most polymorphic species, and E. urophylla displayed the lowest number of polymorphic bands. qPCR analysis in two Eucalyptus species (E. grandis and E. urophylla) and their F₁ hybrids in LTR and internal-domain suggest that some elements have a significant number of complete copies. The F₁ hybrid did not have an intermediate copy number in two families, indicating mechanisms of elimination (or replication) during hybridization. This study represent an initial overview of LTR-RTEs dynamism among Eucalyptus species.

Finnancial support: Cnpq