Isolation And Characterization Of Ty1/copia-like Retrotransposons Of Wild Rice (Zizania Latifolia)

Ty1/copia-like sequences were amplified from Zizania latifolia (Griseb) genomic DNA, by PCR with degenerate oligonucleotide primers corresponding to highly conserved domains in the Ty1/copia-like retrotransposons. PCR fragments of roughly 246bp were isolated and cloned, and 72 clones were obtained. According to alignment and phylogenetic analysis, all sequences were divided into nine groups. Among these families, seven ones were enclosed in phylogenetic tree and two ones had only one sequence respectively and were out of phylogengetic tree. The nucleotide sequence similarity shown by computer analysis between inter- and intra-group was in a wide range, which indicates high level of sequence heterogeneity among these clones and groups. Among these sequences, 29 clones had unique nucleotide sequences (intact sequences), and the others had a frameshift, a stop condon, or both. A phylogenetic analysis comparing these clones with corresponding sequences from other plant species showed that some of the clones are more closely related to rice and common wheat than other species. Southern analysis revealed distribution of these sequences, which also proved that had a closer relationship to rice. Methylation analysis showed there were different levels of methylation in Zizania latifolia, but high level of methylation in rice.