A one-megabase physical map provides insights on gene organization in the enormous mitochondrial genome of cucumber

Genome

Volumn 52, Issue 4, 2009, Pages 299-307

  Bartoszewski, Grzegorz ^a   Gawronski, Piotr ^a   Szklarczyk, Marek ^b   Verbakel, Henk ^c   Havey, Michael J ^d  

^a WARSAW UNIVERSITY OF LIFE SCIENCES   (Poland)

^b UNIVERSITY OF AGRICULTURE IN KRAKOW   (Poland)

^c KEYGENE N V   (Netherlands)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Bacterial artificial chromosome; Cucumis sativus; FPC; Organellar genome

Indexed keywords

MITOCHONDRIAL DNA; PLANT DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME MAP; CUCUMBER; GENETICS; MITOCHONDRIAL GENOME; PLANT GENE; PLANT GENOME;

CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CUCUMIS SATIVUS; DNA, MITOCHONDRIAL; DNA, PLANT; GENES, PLANT; GENOME, MITOCHONDRIAL; GENOME, PLANT;

BACTERIA (MICROORGANISMS); CUCUMIS SATIVUS; EUKARYOTA;

EID: 65349185054     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G09-006     Document Type: Article

References (35)

1. Allen, J.O., Fauron, C.M., Minx, P., Roark, L., Oddiraju, S., Lin, G.N., et al. 2007. Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics, 177:1173-1192. doi:10.1534/genetics.107. 073312. PMID:17660568.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. doi:10.1093/nar/25.17.3389. PMID:9254694.
3. Bartoszewski, G., Katzir, N., and Havey, M.J. 2004a. Organization of repetitive DNAs and the genomic regions carrying ribosomal RNA, cob, and atp9 genes in the cucurbit mitochondrial genomes. Theor. Appl. Genet. 108:982-992. doi:10.1007/s00122-003-1516-5. PMID:15067383.
4. Bartoszewski, G., Malepszy, S., and Havey, M.J. 2004b. Mosaic (MSC) cucumbers regenerated from independent cell cultures possess different mitochondrial rearrangements. Curr. Genet.45:45-53. doi:10.1007/s00294- 003-0456-6. PMID:14586555.
5. Bartoszewski, G., Havey, M.J., Zióikowska, A., and Malepszy, S. 2007. The MSC phenotype of cucumber (Cucumis sativus L.) - a method for production of plant mitochondrial mutants. J. Appl. Genet. 48:1-9. PMID:17272856.
6. Bonen, L. 2008. Cis- and trans-splicing of group II introns in plant mitochondria. Mitochondrion, 8:26-34. doi:10.1016/j.mito. 2007.09.005. PMID:18006386.
7. Burza, W., and Malepszy, S. 1995. Direct plant regeneration from leaf explants in cucumber (Cucumis sativus L.) is free of stable genetic variation. Plant Breed. 114:341-345. doi:10.1111/j. 1439-0523.1995. tb01246.x. Chaw, S.M., Shih, A.C., Wang, D., Wu, Y.W., Liu, S.M., and Chou, T.Y. 2008. The mitochondrial genome of the gymnos-perm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. Mol. Biol. Evol. 25:603-615. doi:10.1093/molbev/msn009. PMID:18192697.
8. Clifton, S.W., Minx, P., Fauron, C.M., Gibson, M., Allen, J.O., Sun, H., et al. 2004. Sequence and comparative analysis of he maize NB mitochondrial genome. Plant Physiol. 136:34863-503. doi:10.1104/pp.104.044602. PMID:15542500. Fauron, C.M. 1995. Maize as a model of higher plant mitochon-drial genome plasticity. Plant Sci. 112:11-32. doi:10.1016/0168-9452(95)04243-N.
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. doi:10.1093/nar/gkg795. PMID:14530439.
10. Havey, M.J. 1997. Paternal transmission of the cucumber mito-chondrial genome. J. Hered. 88:232-235.
11. Havey, M.J., McCreight, J., Rhodes, B., and Taurick, G. 1998. Differential transmission of the cucurbit organellar genomes. Theor. Appl. Genet. 97:122-128. doi:10.1007/s001220050875.
12. Havey, M.J., Park, Y.H., and Bartoszewski, G. 2004. The Psm locus controls paternal sorting of the cucumber mitochondrial genome. J. Hered. 95:492-197. doi:10.1093/jhered/esh081. PMID: 15475394.
13. Hoffmann, M., Dombrowski, S., Guha, C., and Binder, S. 1999. Cotranscription of the rpl5-rps14-cob gene cluster in pea mitochondria. Mol. Gen. Genet. 261:537-545. doi:10.1007/s004380050998. PMID:10323235.
14. Knoop, V., Unseld, M., Marienfeld, J., Brandt, P., Sunkel, S., Ullrich, H., and Brennicke, A. 1996. copia-, gypsy- and LINE-like retrotransposon fragments in the mitochondrial genome of Ara-bidopsis thaliana. Genetics, 142:579-585. PMID:8852855.
15. Cys (GCA). Nucleic Acids Res. 28:2571-2576. doi:10.1093/nar/28.13.2571. PMID:10871408.
16. Lilly, J.W., and Havey, M.J. 2001. Short repetitive motifs contributed significantly to the huge mitochondrial genome of cucumber. Genetics, 159:317-328. PMID:11560907.
17. Lilly, J.W., Bartoszewski, G., Malepszy, S., and Havey, M.J. 2001. A major deletion in the mitochondrial genome sorts with MSC phenotype of cucumber. Curr. Genet. 40:144-151. doi:10.1007/s002940100238. PMID:11680824.
18. Malepszy, S., Burza, W., and Smiech, M. 1996. Characterization of a cucumber (Cucumis sativus L.) somaclonal variant with paternal inheritance. J. Appl. Genet. 37:65-78.
19. Marra, M.A., Kucaba, T.A., Dietrich, N.L., Green, E.D., Brown-stein, B., Wilson, R.K., et al. 1997. High throughput fingerprint analysis of large-insert clones. Genome Res. 7:1072-1084. PMID:9371743.
20. McDermott, P., Connolly, V., and Kavanagh, T.A. 2008. The mito-chondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) contains an integrated linear plas-mid-like element. Theor. Appl. Genet. 117:459-470. doi:10. 1007/s00122-008-0790-7. PMID:18504541.
21. Nakazono, M., and Hirai, A. 1993. Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice. Mol. Gen. Genet. 236:341-346. doi:10.1007/BF00277131. PMID:8437578.
22. Newton, K.J. 1995. Aberrant growth phenotypes associated with mitochondrial genome rearrangements in higher plants. In The molecular biology of plant mitochondria. Edited by C.S. Levings and I.K. Vasil. Kluwer, Amsterdam, The Netherlands. pp. 585-596.
23. Notsu, Y., Masood, S., Nishikawa, T., Kubo, N., Akiduki, G., Na-kazono, M., et al. 2002. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of the flowering plants. Mol. Gen. Genet. 268:434-445.
24. Quinones, V., Zanlungo, S., Moenne, A., Gomez, I., Holuigue, L., Litvak, S., and Jordana, X. 1996. The rpl5-rps14-cob gene arrangement in Solanum tuberosum: rps14 is a transcribed and unedited pseudogene. Plant Mol. Biol. 31:937-943. doi:10. 1007/BF00019483. PMID:8806426.
25. Richardson, A.O., and Palmer, J.D. 2007. Horizontal gene transfer in plants. J. Exp. Bot. 58:1-9. doi:10.1093/jxb/erl148. PMID: 17030541.
26. 0Sanjur, O.I., Piperno, D.R., Andres, T.C., and Wessel-Beaver, L. 2002. Phylogenetic relationships among domesticated and wild species of Cucurbita (Cucurbitaceae) inferred from a mitochon-drial gene: implications for crop plant evolution and areas of origin. Proc. Natl. Acad. Sci. U.S.A. 99:535-540. doi:10.1073/pnas.012577299. PMID:11782554.
27. Soderlund, C., Humphrey, S., Dunham, A., and French, L. 2000. Contigs built with fingerprints, markers, and FPC v4.7. Genome Res. 10:1772-1787. doi:10.1101/gr.GR-1375R. PMID:11076862.
28. Staub, J.E., Chung, S.M., and Fazio, G. 2005. Conformity and genetic relatedness estimation in crop species having a narrow genetic base: the case of cucumber (Cucumis sativus L.). Plant Breed.124:44-53. doi:10.1111/j.1439-0523.2004.01061.x.
29. Stern, D.B. 1987. DNA transposition between plant organellar genomes. J. Cell Sci.7(Suppl.): 145-154.
30. Stern, D.B., and Lonsdale, D.M. 1982. Mitochondrial and chloro-plast genomes of maize have a 12-kilobase DNA sequence in common. Nature (Lond.), 299:698-702. doi:10.1038/299698a0. PMID:6889685.
31. Stern, D.B., and Newton, K.J. 1985. Mitochondrial gene expression in Cucurbitaceae: conserved and variable features. Curr. Genet. 9:395-405. doi:10.1007/BF00421611. PMID:3870928.
32. Stupar, R.M., Lilly, J.W., Town, C.D., Cheng, Z.K., Kaul, S., Buell, C.R., and Jiang, J. 2001. 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. U.S.A.98:5099-5103. doi:10.1073/pnas.091110398. PMID:11309509.
33. Unseld, M., Marienfeld, J.R., Brandt, P., and Brennicke, A. 1997. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat. Genet. 15:57-61. doi:10. 1038/ng0197-57. PMID:8988169.
34. Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., et al. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407-4414. doi:10.1093/nar/23.21.4407. PMID:7501463.
35. Ward, B.L., Anderson, R.S., and Bendich, A.J. 1981. The mito-chondrial genome is large and variable in a family of plants (Cucurbitaceae). Cell, 25:793-803. doi:10.1016/0092-8674(81) 90187-2. PMID:6269758.