Reprogramming of Citrus Retrotransposons during their Early Speciation

Abstract

Speciation of the genus Citrus from a common ancestor has recently been established to begin approximately 8 Mya during the late Miocene, a period of major climatic alterations. In here, we report the changes in activity of Citrus LTR retrotransposons during the process of diversification that gave rise to the current citrus species. To reach this goal, we analyzed four pure species that diverged early during citrus speciation, three recent admixtures derived from those species and an outgroup of the Citrus clade. More than thirty thousand retrotransposons were grouped in 10 linages. Estimations of LTR insertion times revealed that retrotransposon activity followed a species-specific pattern of change that could be ascribed to one of three different models. In some genomes, the expected pattern of gradual transposon accumulation was suddenly arrested during the radiation of the ancestor that gave birth to the current Citrus species. The individualized analyses of retrotransposon lineages showed that in each and every species studied, not all lineages follow the general pattern of the species itself. For instance, inmost of the genomes activity of SIRE elements reached its highest level just before Citrus speciation while Retrofit activity has been steadily growing. Based on these observations we propose that Citrus retrotransposons might respond to those stressful conditions driving speciation as a part of the genetic response involved in adaptation. This proposal implies that the evolving conditions of each species interacts with the internal regulatory mechanisms of the genome controlling the proliferation of mobile elements.