The Mitochondrial Genome of Raphanus sativus and Gene Evolution of Cruciferous Mitochondrial Types

Shengxin Chang; Jianmei Chen; Yankun Wang; Bingchao Gu; Jianbo He; Pu Chu; Rongzhan Guan

doi:10.1016/j.jgg.2013.01.003

Volume 40 Issue 3

Mar. 2013

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The Mitochondrial Genome of Raphanus sativus and Gene Evolution of Cruciferous Mitochondrial Types

doi: 10.1016/j.jgg.2013.01.003

a
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
b
Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, Jurong 212400, China

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Corresponding author: E-mail address: chupu@njau.edu.cn (Pu Chu); E-mail address: guanrzh@njau.edu.cn (Rongzhan Guan)
Received Date: 2012-08-29
Accepted Date: 2013-01-14
Rev Recd Date: 2013-01-09

Available Online: 2013-02-14

Publish Date: 2013-03-20

Abstract

Abstract

To explore the mitochondrial genes of the Cruciferae family, the mitochondrial genome ofRaphanus sativus (sat) was sequenced and annotated. The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes, three rRNA genes and 17 tRNA genes. The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length, which may mediate genome reorganization into two sub-genomic circles, with predicted sizes of 124.8 kb and 115.0 kb, respectively. Furthermore, gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type (mitotype), together with six other reported mitotypes. The cruciferous mitochondrial genomes have maintained almost the same set of functional genes. Compared with Cycas taitungensis (a representative gymnosperm), the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes, but acquired six chloroplast-like tRNAs. Among the Cruciferae, to maintain the same set of genes that are necessary for mitochondrial function, the exons of the genes have changed at the lowest rates, as indicated by the numbers of single nucleotide polymorphisms. The open reading frames (ORFs) of unknown function in the cruciferous genomes are not conserved. Evolutionary events, such as mutations, genome reorganizations and sequence insertions or deletions (indels), have resulted in the non-conserved ORFs in the cruciferous mitochondrial genomes, which is becoming significantly different among mitotypes. This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family. It revealed significant variation in ORFs and the causes of such variation.
- Radish,
- Mitochondrial genome,
- Evolution,
- Cruciferae

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References(31)

References

[1]	Albaum, M., Lührs, R., Trautner, J. et al. Plant Mol. Biol., 29 (1995),pp. 179-185
[2]	Andre, C., Levy, A., Walbot, V. Small repeated sequences and the structure of plant mitochondrial genomes Trends Genet., 8 (1992),pp. 128-132
[3]	Arrieta-Montiel, M.P., Shedge, V., Davila, J. et al. Genetics, 183 (2009),pp. 1261-1268
[4]	Bailey, C.D., Koch, M.A., Mayer, M. et al. Mol. Biol. Evol., 23 (2006),pp. 2142-2160
[5]	Chang, S., Yang, T., Du, T. et al. BMC Genomics, 12 (2011),p. 497
[6]	Chaw, S.M. Mol. Biol. Evol., 25 (2008),pp. 603-615
[7]	Chen, J., Guan, R., Chang, S. et al. PLoS ONE, 10 (2011),p. e17662
[8]	Clifton, S.W., Minx, P., Fauron, C.M. et al. Sequence and comparative analysis of the maize NB mitochondrial genome Plant Physiol., 136 (2004),pp. 3486-3503
[9]	Curtis, I.S. Genetic engineering of radish: current achievements and future goals Plant Cell Rep., 30 (2011),pp. 733-744
[10]	Darling, A.E., Mau, B., Perna, N.T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement PLoS ONE, 5 (2010),p. e11147
[11]	Handa, H. Nucleic Acids Res., 31 (2003),pp. 5907-5916
[12]	Kim, S., Lim, H., Park, S. et al. Theor. Appl. Genet., 115 (2007),pp. 1137-1145
[13]	Kubo, T., Nishizawa, S., Sugawara, A. et al. Nucleic Acids Res., 28 (2000),pp. 2571-2576
[14]	Lee, Y.P., Kim, S., Lim, H. et al. Theor. Appl. Genet., 118 (2009),pp. 719-728
[15]	Lonsdale, D.M., Hodge, T.P., Fauron, C.M. The physical map and organisation of the mitochondrial genome from the fertile cytoplasm of maize Nucleic Acids Res., 12 (1984),pp. 9249-9261
[16]	Makaroff, C.A., Palmer, J.D. Mol. Cell. Biol., 8 (1988),pp. 1474-1480
[17]	Maréchal, A., Brisson, N. Recombination and the maintenance of plant organelle genome stability New Phytol., 186 (2010),pp. 299-317
[18]	Nei, M. Genetic distance between populations Am. Nat., 106 (1972),pp. 283-292
[19]	Newton, K.J., Gabay-Laughnan, S., Paepe, R.D.
[20]	Noreen, Z., Ashraf, M. Environ. Exp. Bot., 67 (2009),pp. 395-402
[21]	Notsu, Y., Masood, S., Nishikawa, T. et al. Mol. Genet. Genomics, 268 (2002),pp. 434-445
[22]	Oda, K., Yamato, K., Ohta, E. et al. Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome J. Mol. Biol., 223 (1992),pp. 1-7
[23]	Palmer, J.D., Shields, C.R. Nature, 307 (1984),pp. 437-440
[24]	Palmer, J.D., Herbon, L.A. Nucleic Acids Res., 14 (1986),pp. 9755-9764
[25]	Sakai, T., Imamura, J. Theor. Appl. Genet., 84 (1992),pp. 923-929
[26]	Schwartz, S., Zhang, Z., Frazer, K.A. et al. PipMaker—a web server for aligning two genomic DNA sequences Genome Res., 10 (2000),pp. 577-586
[27]	Shedge, V., Arrieta-Montiel, M., Christensen, A.C. et al. Plant Cell, 19 (2007),pp. 1251-1264
[28]	Sloan, D.B., Alverson, A.J., Chuckalovcak, J.P. et al. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates PLoS Biol., 10 (2012),p. e1001241
[29]	Tamura, K., Peterson, D., Peterson, N. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Mol. Biol. Evol., 28 (2011),pp. 2731-2739
[30]	Unseld, M., Marienfeld, J.R., Brandt, P. et al. Nat. Genet., 15 (1997),pp. 57-61
[31]	Yamagishi, H., Terachi, T. Genome, 46 (2003),pp. 89-94