Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species.

ABSTRACT: The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatur

SUBMITTER: Zhang QJ 

PROVIDER: S-EPMC5473765 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature