Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome

Nucleic Acids Research

Volumn 33, Issue 19, 2005, Pages 6235-6250

  Ogihara, Yasunari ^a   Yamazaki, Yukiko ^b   Murai, Koji ^c   Kanno, Akira ^d   Terachi, Toru ^e   Shiina, Takashi ^a   Miyashita, Naohiko ^f   Nasuda, Shuhei ^f   Nakamura, Chiharu ^g   Mori, Naoki ^g   Takumi, Shigeo ^g   Murata, Minoru ^h   Futo, Satoshi ⁱ   Tsunewaki, Koichiro ^f,j  

^a KYOTO PREFECTURAL UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c FUKUI PREFECTURAL UNIVERSITY   (Japan)

^d TOHOKU UNIVERSITY   (Japan)

^e KYOTO SANGYO UNIVERSITY   (Japan)

^f KYOTO UNIVERSITY   (Japan)

^g KOBE UNIVERSITY   (Japan)

^h OKAYAMA UNIVERSITY   (Japan)

ⁱ FASMAC Co   (Japan)

^j NONE   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; CEREAL; CHLOROPLAST; CONTROLLED STUDY; EXON; GENE AMPLIFICATION; GENE STRUCTURE; GENOME ANALYSIS; INTRON; MAIZE; MITOCHONDRIAL GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; RICE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; SYNTENY; WHEAT;

BASE SEQUENCE; CHROMOSOME MAPPING; DNA SHUFFLING; DNA, CHLOROPLAST; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENOME, PLANT; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TRITICUM;

TRITICUM AESTIVUM; ZEA MAYS;

EID: 28544439733     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki925     Document Type: Article

References (38)

1. Dewey,R.E., Timothy,D.H. and Levings,C.S.,III (1987) A mitochondrial protein associated with cytoplasmic male sterility in the T cytoplasm of maize. Proc. Natl Acad. Sci. USA, 84, 5374-5378.
2. Miller,R.J. and Koeppe,D.E. (1971) Southern corn leaf blight: susceptible and resistant mitochondria. Science, 173, 67-69.
3. Siculella,L. and Palmer,J.D. (1988) Physical and gene organization of mitochondrial DNA in fertile and male sterile sunflower CMS-associated alterations in structure and transcription of the atpA gene. Nucleic Acids Res., 16, 3787-3799.
4. Cooper,G.M. (2000) The Cell - A Molecular Approach, 2nd edn. Sinauer Assoc., Inc., Sunderland.
5. Oda,K., Yamato,K., Ohta,E., Nakamura,Y., Takemura,M., Nozato,N., Akashi,K., Kanegae,T., Ogura,Y., Kohchi,T. et al. (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA, a primitive form of plant mitochondrial genome. J. Mol. Biol, 223, 1-7.
6. Unseld,M., Marienfeld,J.R., Brandt,P. and Brennicke,A. (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366 924 nucleotides. Nature Genet., 15, 57-62.
7. Cys(GCA). Nucleic Acids Res., 28, 2571-2576.
8. Notsu,Y., Masood,S., Nishikawa,T., Kubo,N., Akiduki,G., Nakazono,M., Hirai,A. and Kadowaki,K. (2002) The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: Frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol. Genet. Genomics, 268, 434-445.
9. Handa,H. (2003) The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): Comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res., 31, 5907-5916.
10. Clifton,S.W., Minx,P., Fauron,C.M., Gibson,M., Allen,J.O., Sun,H., Thompson,M., Barbazuk,W.B., Kanuganti,S., Tayloe,C. et al. (2004) Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol., 136, 3486-3503.
11. Sugiyama,Y., Watase,Y., Nagase,M., Makita,N., Yagura,S., Hirai,A. and Sugiura,M. (2005) The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: Comparative analysis of mitochondrial genomes in higher plants. Mol. Genet. Genomics, 272, 603-615.
12. Andre,C., Levy,A. and Walbot,V. (1992) Samll repeated sequences and the structure of plant mitochondrial genomes. Trends Genet., 8, 128-132.
13. Bendich,A.J. (1993) Reaching for the ring: The study of mitochondrial genome structure. Curr. Genet., 24, 279-290.
14. Palmer,J.D. and Shields,C.R. (1984) Tripartite structure of the Brassica campestris mitochondrial genome. Nature, 307, 437-440.
15. Quetier,F., Lejeune,B., Delorme,S., Falconet,D. and Jubier,M.F. (1985) Molecular form and function of the wheat mitochondrial genome. In Van Vloten-Doting,L., Groot,G.S.P. and Hall,T.C. (eds), Molecular Form and Function of the Plant Genome. Plenum Press, NY, pp. 413-420.
16. Lonsdale,D.M., Brear,T., Hodge,T.P., Melville,S.E. and Rottmann,W.H. (1988) The plant mitochondrial genome: Homologous recombination as a mechanism for generating heterogeneity. Philos. Trans. R. Soc. Lond. B Biol. Sci, 319, 149-163.
17. Fauron,C., Casper,M., Gao,Y. and Moore,B. (1995) The maize mitochondrial genome: Dynamic, yet functional. Trends Genet., 11, 228-235.
18. Ogihara,Y. and Tsunewaki,K. (1988) Diversity and evolution of chloroplast DNA in Triticum and Aegilops as revealed by restriction fragment analysis. Theor. Appl. Genet., 76, 321-332.
19. Wang,G.-Z., Matsuoka,Y. and Tsunewaki,K. (2000) Evolutionary features of chondriome divergence in Triticum (wheat) and Aegilops shown by RFLP analysis of mitochondrial DNAs. Theor. Appl. Genet., 100, 221-231.
20. Tsunewaki,K. (1996) Plasmon analysis as the counterpart of genome analysis. In Jauhar,P.P. (ed.), Methods of Genome Analysis in Plants. CRC Press, NY, pp. 271-299.
21. Ogihara,Y., Isono,K., Kojima,T., Endo,A., Hanaoka,M., Shiina,T., Terachi,T., Utsugi,S., Murata,M., Mori,N. et al. (2000) Chinese Spring wheat (Triticum aestivum L.) chloroplast genome: Complete sequence and contig clones. Plant Mol. Biol. Rep., 18, 243-253.
22. Bonen,L. and Gray,M.W. (1980) Organization and expression of the mitochondrial genome of plants. I. The genes for wheat mitochondrial ribosomal and transfer RNA: Evidence for an unusual arrangement. Nucleic Acids Res., 8, 319-335.
23. Kolodner,R. and Tewari,K.K. (1975) The molecular size and conformation of the chloroplast DNA from higher plants. Biochim. Biophys. Acta,, 402, 372-390.
24. Bonen,L. (1995) The wheat mitochondrial genome. In Levings,C.S.III and Vasil,I.K. (eds), The Molecular Biology of Plant Mitochondria. Kluwer Academic Publ., Netherlands, pp. 345-364.
25. Altshul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol, 215, 403-410.
26. Lowe,T.M. and Eddy,S.R. (1997) tRNA scan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
27. Bonen,L. and Bird,S. (1988) Sequence analysis of the wheat mitochondrial atp6 gene reveals a fused upstream reading frame and markedly divergent N-termini among plant ATP6 proteins. Gene, 73, 47-56.
28. Stern,D.B. and Palmer,J.D. (1984) Recombination sequences in plant mitochondrial genomes: Diversity and homologies to known mitochondrial genes. Nucleic Acids Res., 12, 6141-6157.
29. Joyce,P.B.M., Spencer,D.F., Bonen,L. and Gray,M.W. (1988) Genes for tRNA-Asp, tRNA-Pro, tRNA-Tyr and two tRNAs-Ser in wheat mitochondrial DNA. Plant Mol. Biol., 10, 251-262.
30. Joyce,P.B.M. and Gray,M.W. (1989) Chloroplast-like transfer RNA genes expressed in wheat mitochondria. Nucleic Acids Res., 17, 5461-5476.
31. Falconet,D., Lejeune,B., Quetier,F. and Gray,M.W. (1984) Evidence for homologous recombination between repeated sequences containing 18S and 5S ribosomal RNA genes in wheat mitochondrial DNA. EMBO J., 3, 297-302.
32. Lejeune,B., Delorme,S., Delcher,E. and Quetier,E. (1987) Recombination in wheat mitochondrial DNA: Occurrence of nine different genomic contexts for the 18S-5S genes. Plant Physiol. Biochem., 25, 227-233.
33. Fauron,C. and Havlik,M. (1989) The maize mitochondrial genome of the normal type and the cytoplasmic male sterile type T have very different organization. Curr. Genet., 15, 149-154.
34. Goulding,S.E., Olmstead,R.G., Morden,C.W. and Wolfe,K.H. (1996) Ebb and flow of the chloroplast inverted repeat. Mol. Gen. Genet., 252, 195-206.
35. Arrieta-Montiel,M., Lyznik,A., Woloszynska,M., Janska,H., Tohme,J. and Mackenzie,S. (2001) Tracing evolutionary and developmental implications of mitochondrial stoichiometric shifting in the common bean. Genetics, 158, 851-864.
36. Hiratsuka,J., Shimada,H., Whittier,R., Ishibashi,T., Sakamoto,M., Mori,M., Kondo,C., Honji,Y., Sun,C.-R., Meng,B.-Y. et al. (1989) 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. Mol. Gen. Genet., 217, 185-194.
37. Maier,R.M., Neckermann,K., Igloi,G.L. and Kossel,H. (1995) Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol., 251, 614-628.
38. Backert,S., Dorfel,P., Lurz,R. and Borner,T. (1996) Rolling-circle replication of mitochondrial DNA in the higher plant Chenopodium album (L.). Mol. Cell. Biol., 16, 6285-6294.