Copia-Like Retrotransposons in the Rice Genome: Few and Assorted

We performed a comprehensive analysis of Ty1-copia-like retrotransposons in about 10% of the Oryza sativa genome and identified 100 elements. These were divided into nine classes by their reverse transcriptase similarity and into 39 families according to the sequences of their long terminal repeats (LTRs). The deduced total number of copia-like elements in rice is ~1000, comprising 1.7% of the genome. Solo LTRs and truncated elements comprise an additional 2.3% of the genome. This is low compared with other plants, especially grasses, but comparable to Arabidopsis. However, the total number of families in the genome, at least 50, is similar to that in other plants. At least some of these classes are present in the genomes of other grasses, and related elements can be found in dicotyledonous plants. The transcriptional activity of each family was estimated by searching for homologous expressed sequence tags in databases. No correlation was found between the number of homologous expressed sequence tags and family size. In comparison with the copia retrotransposons, 222 gypsy-like and 66 LINE-like retroelements, as well as five pararetrovirus-like elements, were found, corresponding to about 2220, 660, and 50, respectively, in the genome. A low rate of retrotransposon transcription and a high rate of loss of integrated copies by ectopic, intrachromosomal recombination are proposed as the reasons for the paucity of retrotransposons in the rice genome.