Variation of 16S-23S internally transcribed spacer sequence and intervening sequence in rDNA among the three major Agrobacterium species

Abstract

We analyzed 16S-23S internally transcribed spacer (ITS) and neighboring sequences among 37 strains belonging to the three major pathogenic Agrobacterium species, in order to know variation in each species and to develop a simple discrimination method. Number of ITS size variation was 9, 4, and 7 in Agrobacterium tumefaciens, Agrobacterium vitis, and Agrobacterium rhizogenes, respectively. The ITS sequence of most strains in each species was distinguishable from that of the other two species. The region surrounded by 16S rRNA gene and trn(Ala) contained information to distinguish between the ITS variants and was easy for sequencing. Intervening sequences (IVSs) in 23S rRNA gene were classified into short and long types in each species. Some long-type IVSs of A. vitis were very similar to that of A. tumefaciens, while the other long-type IVSs of A. vitis were very similar to that of A. rhizogenes. Two A. vitis strains simultaneously contained both types of IVS. Similarly, the two exceptional A. vitis strains possessed A. tumefaciens-type ITS in addition to A. vitis-type ITS. These results suggest horizontal transfer of rDNA and subsequent recombination. Among the three species, A. tumefaciens was most variable based on 16S rRNA gene, ITS and IVS sequences.