Sample Sequence Analysis of Grass Genomes Indicates Frequent and Repeated Horizontal Transfer of LTR-Retrotransposons

LTR-retrotransposons are one of the most important components of plant genomes. A few studies have compared their properties across multiple “fully sequenced” genomes, but this requirement for a genome assembly means that only a small number of taxa can currently be investigated. To demonstrate an approach for comprehensive comparative analysis of LTR-retrotransposons across thousands of species, we generated low-depth sample sequence data for 19 previously-uncharacterized genomes from the panicoid grass subfamily. From the analysis, we identified highly dynamic changes in the activity of numerous LTR-retrotransposon families. The three Ty3/Gypsy families Milt, Xilon-Diguus, and Grande were found to be particularly variable, exhibiting very different compositions even among closely related species. Numerous cases of lineage-specific activation and extinctions of specific LTR-retrotransposon families were observed. Using 62 public plant genome sequences and the 19 panicoid sample sequences, we investigated the possible horizontal transfer of LTR-retrotransposons. We found that the genus Oryza has had many horizontal transfers with the panicoids, including at least 24 separate horizontal transfers involving 11 Oryza species and 19 panicoid species. Among the 11 Oryza species, Oryza sativa indica exhibited an extraordinarily highly frequency of horizontal transfer with the lineage including Echinochloa haploclada.