Pseudogenes and short repeated sequences in the rice chloroplast genome.

The rice chloroplast genome has been derived from a tobacco-like ancestral form by three major inversions. In the rice genome we have found six pseudogenes, psi trnG, psi trnI, psi 3'-rps 12a, psi trnT, psi trnE and psi trnfM/G, all located near inversion endpoints, as well as four short repeated sequences. A comparison of rice, wheat and tobacco sequences indicated that similar pseudogenes are present in wheat but not in tobacco, suggesting that the creation of these pseudogenes occurred before the divergence of rice and wheat. The region downstream of rbcL is a variable region and contains psi rpl23 in rice and wheat and another psi 3'-rps 12b further downstream in rice. This psi 3'-rps 12b shows a higher homology to the functional rps 12 than psi 3'-rps 12a, which suggests that it appeared more recently. The involvement of these pseudogenes in genome inversions and the creation of the pseudogenes and short repeated sequences are discussed.