Figure 4

Pack-MuLEs movements in allotetraploid Oryza minuta and its diploid ancestors. Through comparative genomic analysis, we identified one Pack-MuLE specifically inserted into the BBCC_BB subgenome. FGENESH predicted one specific gene model within this MuLE element, named MB6 (a). We aligned the captured sequence of this MuLE with the japonica reference genome and found that this MuLE probably captured sequences from multiple loci. This region (~1,100 bp) has high identity with 07 g37840 (94% identity), which produced a novel ORF by integration with some unknown sequences (b). At the same genomic region of the CC subgenome in O. minuta, we identified the same type of MuLE with different foreign sequences (118 bp in length and lacking an exact homologous sequence in the japonica genome) (a). These two MuLEs share a highly identical 3′ sequence and a relatively divergent 5′ sequence (probably caused by other TE insertions). The presence of completely different TSD sequences suggests that these insertion events occurred independently (b).