The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowering plants: A genome-wide investigation of indica rice

Journal of Molecular Evolution

Volumn 64, Issue 3, 2007, Pages 299-307

  Tian, Xiangjun ^a,b   Zheng, Jing ^c   Hu, Songnian ^a,b   Yu, Jun ^a,b,d  

^a Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^d Beijing Airport Industrial Zone B 6   (China)

Author keywords

Flowering plants; Mitochondrion; Nucleus; Oryza sativa; Plastid; tRNA gene transfer

Indexed keywords

TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; FLOWERING; GENE TRANSFER; GENOME; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASTID; RICE;

CELL NUCLEUS; EVOLUTION, MOLECULAR; FLOWERS; GENES, PLANT; GENOME, PLANT; MITOCHONDRIA; ORYZA SATIVA; PHYLOGENY; PLASTIDS; RECOMBINATION, GENETIC; RNA, TRANSFER;

MAGNOLIOPHYTA; ORYZA SATIVA;

EID: 33847650857     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0200-6     Document Type: Article

References (25)

1. Bensasson D, Zhang D, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol 16:314-321
2. Blanchard JL, Schmidt GW (1996) Mitochondrial DNA migration events in yeast and humans: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. Mol Biol Evol 13:893
3. Ceci LR, Saiardi A, Siculella L, Quagliariello C (1993) A tRNA (Val) (GAC) gene of chloroplast origin in sunflower mitochondria is not transcribed. Plant Mol Biol 23:727-736
4. Cho Y, Mower JP, Qiu YL, Palmer JD (2004) Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci USA 101:17741-17746
5. Dietrich A, Weil JH, Marechal-Drouard L (1992) Nuclear-encoded transfer RNAs in plant mitochondria. Annu Rev Cell Biol 8:115-131
6. Fey J, Dietrich A, Cosset A, Desprez T, Marechal-Drouard L (1997) Evolutionary aspects of "chloroplast-like" trnN and trnH expression in higher-plant mitochondria. Curr Genet 32:358-360
7. Joyce PB, Gray MW (1989) Chloroplast-like transfer RNA genes expressed in wheat mitochondria. Nucleic Acids Res 17:5461-5476
8. Kumar R, Marechal-Drouard L, Akama K, Small I (1996) Striking differences in mitochondrial tRNA import between different plant species. Mol Gen Genet 252:404-411
9. Lopez JV, Yuhki N, Masuda R, Modi W, O'Brien SJ (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39:174-190
10. Marechal-Drouard L, Guillemaut P, Cosset A, Arbogast M, Weber F, Weil JH, Dietrich A (1990) Transfer RNAs of potato (Solanum tuberosum) mitochondria have different genetic origins. Nucleic Acids Res 18:3689-3696
11. Marechal-Drouard L, Weil JH, Dietrich A (1993) Transfer RNAs and transfer RNA genes in plants. Annu Rev Plant Physiol Plant Mol Biol 44:13-32
12. Miyata S, Nakazono M, Hirai A (1998) Transcription of plastid-derived tRNA genes in rice mitochondria. Curr Genet 34:216-220
13. Nugent JM, Palmer JD (1991) RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell 66:473-481
14. Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu YL, Song K (2000) Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci USA 97:6960-6966
15. Richly E, Leister D (2004a) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21:1081-1084
16. Richly E, Leister D (2004b) NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs. Mol Biol Evol 21:1972-1980
17. Small I, Adams KL, Chapron A, Dietrich A, Duchene AM, Lancelin D, Marechal-Drouard L, Menand B, Mireau H, Moudden Y, Ovesna J, Peeters N, Sakamoto W, Souciet G, Wintz H (1999) The strange evolutionary history of plant mitochondiral tRNAs and their aminoacyl-tRNA synthetases. J Hered 90:333-337
18. Tang J, Xia H, Cao M, Zhang X, Zeng W, Hu S, Tong W, Wang J, Yu J, Yang H, Zhu L (2004) A comparison of rice chloroplast genomes. Plant Physiol 135:412-420
19. Tian X, Zheng J, Hu S, Yu J (2006) The rice mitochondrial genomes and their variations. Plant Physiol 140:401-410
20. Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123-135
21. Veronico P, Gallerani R, Ceci LR (1996) Compilation and classification of higher plant mitochondrial tRNA genes. Nucleic Acids Res 24:2199-2203
22. Woischnik M, Moraes CT (2002) Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Res 12:885-893
23. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713
24. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Li J, Liu Z, Qi Q, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Zhao W, Li P, Chen W, Zhang Y, Hu J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Tao M, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92
25. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Xiao Y, Bu D, Tan J, Yang L, Ye C, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Huang X, Su Z, Tong W, Tong Z, Ye J, Wang L, Lei T, Chen C, Chen H, Huang H, Zhang F, Li N, Zhao C, Huang Y, Li L, Xi Y, Qi Q, Li W, Hu W, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wong GK, Yang H (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38