Molecular and General Genetics MGG

, Volume 217, Issue 2–3, pp 185–194 | Cite as

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

  • 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
  • Masahiro Sugiura
Article

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.

Key words

Conserved open reading frames Monocots Chloroplast DNA Sequence duplication Multimer formation 

Abbreviations

PSII

photosystem II

PSI

photosystem I

RuBisCo

ribulose 1,5-bisphosphate carboxylase

IRA and IRB

denote the inverted repeat regions distal and proximal tondhF respectively

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Copyright information

© Springer-Verlag 1989

Authors and Affiliations

  • Junzou Hiratsuka
    • 1
  • Hiroaki Shimada
    • 1
  • Robert Whittier
    • 1
  • Takashi Ishibashi
    • 1
  • Masahiro Sakamoto
    • 1
  • Masao Mori
    • 1
  • Chihiro Kondo
    • 1
  • Yasuko Honji
    • 1
  • Chong-Rong Sun
    • 3
  • Bing-Yuan Meng
    • 1
  • Yu-Qing Li
    • 1
  • Akira Kanno
    • 2
  • Yoko Nishizawa
    • 2
  • Atsushi Hirai
    • 2
  • Kazuo Shinozaki
    • 1
  • Masahiro Sugiura
    • 1
  1. 1.Center for Gene ResearchNagoya UniversityNagoyaJapan
  2. 2.Faculty of AgricultureNagoya UniversityNagoyaJapan
  3. 3.Department of BiochemistryFudan UniversityShanghaiChina

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