Gene duplication and transfer events in plant mitochondria genome

Biochemical and Biophysical Research Communications

Volumn 376, Issue 1, 2008, Pages 1-4

  Xiong, Ai Sheng ^a   Peng, Ri He ^a   Zhuang, Jing ^a   Gao, Feng ^a   Zhu, Bo ^a   Fu, Xiao Yan ^a   Xue, Yong ^a   Jin, Xiao Fen ^a   Tian, Yong Sheng ^a   Zhao, Wei ^a   Yao, Quan Hong ^a  

^a INSTITUTE OF EDIBLE FUNGI   (China)

Author keywords

Evolution; Gene duplication; Mitochondria; Plant; Transfer

Indexed keywords

GENE DUPLICATION; GENE TRANSFER; GENOME; MITOCHONDRIAL GENE; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; SHORT SURVEY;

EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, MITOCHONDRIAL; GENOME, PLANT;

EID: 52049098666     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.08.116     Document Type: Short Survey

References (55)

1. Henze K., and Martin W. Evolutionary biology: essence of mitochondria. Nature 426 (2003) 127-128
2. McBride H.M., Neuspiel M., and Wasiak S. Mitochondria: more than just a powerhouse. Curr. Biol. 16 (2006) R551-R560
3. Schwartz M., and John V.J. Paternal Inheritance of Mitochondrial DNA. N. Engl. J. Med. 347 (2002) 576-580
4. Gray M.W. The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141 (1992) 233-357
5. Maple J., and Møller S.G. Plastid division: evolution, mechanism and complexity. Ann. Bot. 99 (2007) 565-579
6. Palmer J.D., and Herbon L.A. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J. Mol. Evol. 28 (1989) 87-97
7. Burger G., Lavrov D.V., Forget L., and Lang B.F. Sequencing complete mitochondrial and plastid genomes. Nat. Protoc. 2 (2007) 603-614
8. Mereu P., Palici di Suni M., Manca L., and Masala B. Complete nucleotide mtDNA sequence of Barbary sheep (Ammotragus lervia). DNA Seq. 19 3 (2008) 241-245 Jun
9. Notsu Y., Masood S., Nishikawa T., Kubo N., Akiduki G., Nakazono M., Hirai A., and Kadowaki K. 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 (2002) 434-445
10. Sugiyama Y., Watase Y., Nagase M., Makita N., Yagura S., Hirai A., and Sugiura M. The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol. Genet. Genomics 272 (2005) 603-615
11. Ohno S. Evolution by Gene Duplication (1970), Springer, New York
12. Hoshino A., Johzuka H.Y., and Iida S. Gene duplication and mobile genetic elements in the morning glories. Gene 265 (2001) 1-10
13. Taylor J.S., Van de Peer Y., and Meyer A. Genome duplication, divergent resolution and speciation. Trends Genet. 17 (2001) 299-301
14. Lynch M., and Conery J.S. The evolutionary fate and consequences of duplicate genes. Science 290 (2000) 1151-1155
15. Simillion C., Vandepoele K., Van Montagu M.C., Zabeau M., and Van de Peer Y. The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 99 (2002) 13627-13632
16. He X., and Zhang J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169 (2005) 1157-1164
17. Lynch M., and Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics 154 (2000) 459-473
18. Causier B., Castillo R., Zhou J., Ingram R., Xue Y., Schwarz S.Z., and Davies B. Evolution in action: following function in duplicated floral homeotic genes. Curr. Biol. 15 (2005) 1508-1512
19. Shimeld S.M. Gene function, gene networks and the fate of duplicated genes. Semin. Cell Dev. Biol. 10 (1999) 549-553
20. Taylor J.S., and Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. 38 (2004) 615-643
21. Samonte R.V., and Eichler E.E. Segmental duplications and the evolution of the primate genome. Nat. Rev. Genet. 3 (2002) 65-72
22. Wolfe K.H., and Li W.H. Molecular evolution meets the genomics revolution. Nat. Genet. 33 (2003) 255-265
23. Hurley I., Hale M.E., and Prince V.E. Duplication events and the evolution of segmental identity. Evol. Dev. 7 (2005) 556-567
24. Sémon M., and Wolfe K.H. Consequences of genome duplication. Curr. Opin. Genet. Dev. 17 (2007) 505-512
25. Koszul R., Caburet S., Dujon B., and Fischer G. Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J. 23 (2004) 234-243
26. Koszul R., Dujon B., and Fischer G. Stability of large segmental duplications in the yeast genome. Genetics 172 (2006) 2211-2222
27. Wendel J.F. Genome evolution in polyploids. Plant Mol. Biol. 42 (2000) 225-249
28. Blanc G., and Wolfe K.H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16 (2004) 1667-1678
29. Yuan Q., Hill J., Hsiao J., Moffat K., Ouyang S., Cheng Z., Jiang J., and Buell C.R. Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol. Genet. Genomics 267 (2002) 713-720
30. Lang B.F., Gray M.W., and Burger G. Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet. 33 (1999) 351-397
31. Martin W., Deusch O., Stawski N., Grünheit N., and Goremykin V. Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends Plant Sci. 10 (2005) 203-209
32. Unseld M., Marienfeld J.R., Brandt P., and Brennicke A. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat. Genet. 15 (1997) 57-61
33. Havey M.J., Lilly J.W., Bohanec B., Bartoszewski G., and Malepszy S. Cucumber: a model angiosperm for mitochondrial transformation?. J. Appl. Genet. 43 (2002) 1-17
34. Ward B.L., Anderson R.S., and Bendich A.J. The mitochondrial genome is large and variable in a family of plants (cucurbitaceae). Cell 25 (1981) 793-803
35. Lilly J.W., and Havey M.J. Small, repetitive DNAs contribute significantly to the expanded mitochondrial genome of cucumber. Genetics 159 (2001) 317-328
36. Palmer J.D., and Herbon L.A. Unicircular structure of the Brassica hirta mitochondrial genome. Curr. Genet. 11 (1987) 565-570
37. Albert B., Godelle B., and Gouyon P. Evolution of the plant mitochondrial genome: dynamics of duplication and deletion of sequences. J. Mol. Evol. 46 (1998) 155-158
38. Small I.D., Suffolk R., and Leaver C.J. Evolution of plant mitochondrial genomes via substoichiometric intermediates. Cell 58 (1989) 69-76
39. Fauron C.M.R., Moore B., and Casper M. Maize as a model of higher plant mitochondrial genome plasticity. Plant Sci. 112 (1995) 11-32
40. Handa H. 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 (2003) 5907-5916
41. Liu S.L., and Adams K. Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids. BMC Evol. Biol. 8 (2008) 25
42. Adams K.L., Qiu Y.L., Stoutemyer M., and Palmer J.D. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc. Natl. Acad. Sci. USA 99 (2002) 9905-9912
43. Sato S., Nakamura Y., Kaneko T., Asamizu E., and Tabata S. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6 (1999) 283-290
44. The Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature 408 (2000) 796-815.
45. Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., and Mori M. 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 (1989) 185-194
46. Yu J., Hu S., Wang J., Wong G.K., Li S., and Liu B. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 (2002) 79-92
47. Rujan T., and Martin W. How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet. 17 (2001) 113-120
48. Bergthorsson U., Adams K.L., Thomason B., and Palmer J.D. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424 (2003) 197-201
49. Sun C.W., and Callis J. Recent stable insertion of mitochondrial DNA into an Arabidopsis polyubiquitin gene by nonhomologous recombination. Plant Cell 5 (1993) 97-107
50. Blanchard J.L., and Schmidt G.W. Pervasive migration of organellar DNA to the nucleus in plants. J. Mol. Evol. 41 (1995) 397-406
51. Stupar R.M., Lilly J.W., Town C.D., Cheng Z., Kaul S., Buell C.R., and Jiang J. Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc. Natl. Acad. Sci. USA 98 (2001) 5099-5103
52. Lin X., Kaul S., Rounsley S., Shea T.P., Benito M.I., Town C.D., Fujii C.Y., and Mason T. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402 (1999) 761-768
53. Kubo N., Takano M., Nishiguchi M., and Kadowaki K. Mitochondrial sequence migrated downstream to a nuclear V-ATPase B gene is transcribed but non-functional. Gene 271 (2001) 193-201
54. Kumar R., Drouaud J., Raynal M., and Small I. Characterization of the nuclear gene encoding chloroplast ribosomal protein S13 from Arabidopsis thaliana. Curr. Genet. 28 (1995) 346-3520
55. Mollier P., Hoffmann B., Debast C., and Small I. The gene encoding Arabidopsis thaliana mitochondrial ribosomal protein S13 is a recent duplication of the gene encoding plastid S13. Curr. Genet. 40 (2002) 405-409