p-SINE1-like intron of the CatA catalase homologs and phylogenetic relationships among AA-genome Oryza and related species

Intron-2 of the Oryza sativa CatA catalase gene is similar in nucleotide se quence to p-SINE1, a retroposon, and seems to have been added to the ancest ral genome of rice. To examine when the p-SINE1-like intron was inserted in to CatA during the evolutionary divergence of Oryza species, and to elucida te the evolutionary relationships among Oryza species using the sequence of the intron as a marker, we performed polymerase chain reaction (PCR) analy ses of 32 accessions of 17 Oryza species with various genome types. Agarose -gel electrophoresis of the PCR products revealed that all the Oryza specie s with an AA genome have the CatA homolog with the intron, whereas other Or yza species have the CatA homolog without the intron. These results indicat e that intron-2 of CatA is a good marker for distinguishing species with an AA genome among Oryza species. Sequencing of the PCR products showed that all the introns are similar to p-SINE1, though with slight variations in le ngth. We also performed PCR analyses using four accessions of three species in genera related to Oryza, and found that there is an intron in the CatA homolog of Leersia perrieri. On the other hand, the CatA homolog of Portere sia coarctata has no intron. Sequence data showed that the L. perrieri homo log has a p-SINE1-like intron similar to that in Oryza species with an AA g enome. These results suggest that the p-SINE1-like intron was already prese nt in the common ancestor of Oryza and L. perrieri and was then lost in the ancestors of P. coarctata and of the Oryza species other than those with a n AA genome. The phylogenetic tree of Oryza species with an AA genome based on the nucleotide sequences of the introns leads us to propose that Oryza species with an AA genome evolved from an ancestor of Oryza longistaminata.