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It is possible to apply DNA sequencing data of A. oryzae RIB40 (Tominaga et al, 2006) to investigation of genomic structure of homologous gene cluster in 210 A. oryzae RIB strains. Using PCR technique, 210 A. oryzae RIB strains were easily classified into groups 1, 2, and 3, and others according to amplified patterns with seven aflatoxin homologous genes. Group 1 (122 strains, 58.1%) strains conserve intact aflatoxin biosynthesis gene homolog cluster. Group 2 (77 strains, 36.7%) and group 3 strains (9 strains, 4.3%) reveal large deletions of the aflatoxin gene homolog cluster, which is more than half. It is possible that the breakpoint within the cluster of group 2 strains would be near the ver-1gene, as described by Kusumoto et al. (2000). Two strains (0.9 %) that could not be classified into group 1, 2, and 3 were called "others". The majority of A. oryzae RIB strains (94.8 %) are categorized as groups 1 and 2. Murakami (1971) has evaluated 20 mycological characters of RIB strains, graded them from 1 to 6 and also proved no aflatoxin production in all strains. To examine the differences between group 1 and group 2 based on phenotype, analysis of variance was performed. Significant differences among 19 characters except for the aflatoxigenic character were recognized with 5 characters (length of stalk, color of old slant culture, roughness of conidia, coloration of hydroquinone, and pink color of conidia in medium with anisic acid). The length of stalk of group 1 was longer than that of group 2 at level of p<0.01 (data not shown). Therefore, this PCR analysis is a useful method for classification at intra-species level. Furthermore, it is safe for the food fermentation and enzyme industry to use A. oryzae especially groups 2 and 3 strains since these strains revealed absolute lack of aflatoxigenic ability at the molecular level. From the results of DNA sequencing analysis between A. oryzae RIB40 belonging to group 1 and RIB62 belonging to group 2, RIB62 shows a large deletion upstream of ver-1 homolog with more than half of the aflatoxin homologous gene cluster being missing. Adjacent to the deletion of the aflatoxin homologous gene cluster, RIB62 has a "unique sequence" of about 8-kb and a telomere. We investigated whether homologues of the unique sequence region of A. oryzae RIB62 were present in other group strains with Southern blot analysis. At first, we performed Southern blot analysis of 210 A. oryzae RIB strains with "no-hit" probe of unique sequence. The results showed that all group 2 strains had an identical size of signal of about 9.4-kb, while in other group strains different size of hybridizing signals from that of group 2 strains or with no signal were detected (data not shown).Subsequently, to confirm the presence of the unique sequence, Southern blot analysis with the four kinds of probe, which were derived from the unique sequence of RIB62 was performed for 16 selected strains from group 1, 2, and 3. Group 1 strains showed various signal patterns; double or single band(s) in most strains and with no signal in RIB40. In addition, the signal pattern of group 1 strains was different according to the probe used. However all group 2 strains showed an identical band of about 9.4 kbin all the cases when the four probes were used. In the group 3 strains, no signal was detected with the four probes. Therefore, 8-kb unique sequence of RIB62 is conserved in A. oryzae group 2 strains and present partially in some group 1 strains. To investigate the chromosomal position of the unique sequence, chromosomal Southern analysis was performed using four kinds of probe, US 1 to 4. Separation of the chromosomes of selected eight of A. oryzae group 1 and group 2 strains by clamped homogeneous electric field (CHEF) revealed different karyotype (data not shown). Among them, RIB62 showed a unique band of about 3 Mb, whereas other strains have no this chromosome. The detected signal(s) in A. oryzae group 1 strains were revealed in two or one chromosome(s) and in no signal in RIB40, while that of group 2 strains showed in single chromosome with four kinds of probes. The signal patterns of group 1 strains were different according to the probe used, while those of group 2 strains were identical. These results are almost identical to those of genomic Southern blot analysis To confirm the structure of the region flanking the partial aflatoxin homologous gene cluster in A. oryzae group 2 strains, we investigated the pattern of PCR amplification in 210 A. oryzae RIB strains with a set of primers designed to amplify between ver-1 and the unique sequence. The oligonucleotide primer for the ver-1 side was common to both RIB 40 and RIB62, while that of the unique sequence side was derived from RIB62. From the results of PCR with this set of primers, a fragment of about 1 kb was amplified from all group 2 strains and none of strains from other group generated PCR products. Therefore, it is possible to distinguish group 2 strains from other group strains with this set of primers. Southern blotting and PCR analysis resulted that all group 2 strains has the identical "unique sequence" and genomic structure of deletion including flaking region. In addition, this characterization of group 2 strains could be applied to distinguish this group strainsfrom the other group strains. The result of chromosomal Southern analysis (data not shown) suggested that the aflatoxin homologous gene cluster and the "unique sequence"existed on the same chromosome in groups 1 strains having these two portions. Taken together, A. oryzae group 2 strains might have differentiated from the ancestral strain due to chromosomal breakage. Although it is extremely difficult to determine the reason for the non-aflatoxigenicity of A. oryzae from the analysis of the genomic structure, this dissertation may provide basic molecular information for the profound approaches. In succession, further research on aflR protein activity or other related signal transduction pathway and the deleted aflatoxin biosynthesis gene homolog cluster of group 2 strains together with group 3 strains may help in clarifying the mechanism of the cluster deletion and differentiation.