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The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals
Authors:Junzou Hiratsuka  Hiroaki Shimada  Robert Whittier  Takashi Ishibashi  Masahiro Sakamoto  Masao Mori  Chihiro Kondo  Yasuko Honji  Chong-Rong Sun  Bing-Yuan Meng  Yu-Qing Li  Akira Kanno  Yoko Nishizawa  Atsushi Hirai  Kazuo Shinozaki and Masahiro Sugiura
Institution:(1) Center for Gene Research, Nagoya University, Chikusa, 464-01 Nagoya, Japan;(2) Faculty of Agriculture, Nagoya University, Chikusa, 464-01 Nagoya, Japan;(3) Present address: Department of Biochemistry, Fudan University, Shanghai, China
Abstract:Summary The entire chloroplast genome of the monocot rice (Oryza sativa) has been sequenced and comprises 134525 bp. Predicted genes have been identified along with open reading frames (ORFs) conserved between rice and the previously sequenced chloroplast genomes, a dicot, tobacco (Nicotiana tabacum), and a liverwort (Marchantia polymorpha). The same complement of 30 tRNA and 4 rRNA genes has been conserved between rice and tobacco. Most ORFs extensively conserved betweenN. tabacum andM. polymorpha are also conserved intact in rice. However, several such ORFs are entirely absent in rice, or present only in severely truncated form. Structural changes are also apparent in the genome relative to tobacco. The inverted repeats, characteristic of chloroplast genome structure, have expanded outward to include several genes present only once per genome in tobacco and liverwort and the large single copy region has undergone a series of inversions which predate the divergence of the cereals. A chimeric tRNA pseudogene overlaps an apparent endpoint of the largest inversion, and a model invoking illegitimate recombination between tRNA genes is proposed which accounts simultaneously for the origin of this pseudogene, the large inversion and the creation of repeated sequences near the inversion endpoints.
Keywords:Conserved open reading frames  Monocots  Chloroplast DNA  Sequence duplication  Multimer formation
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