Comparison of mitochondrial and chloroplast genome segments from three onion (Allium cepa L.) cytoplasm types and identification of a trans-splicing intron of cox2

Current Genetics

Volumn 56, Issue 2, 2010, Pages 177-188

  Kim, Sunggil ^a   Yoon, Moo Kyoung ^b  

^a Chonnam National University   (South Korea)

^b Rural Development Administration   (South Korea)

Author keywords

Cox2; Cytoplasmic male sterility (CMS); Onion (Allium cepa L.); Substoichiometric shifting; Trans splicing

Indexed keywords

CHLOROPLAST DNA; CYCLOOXYGENASE 2; MITOCHONDRIAL PROTEIN; PROTEIN ATP6; PROTEIN COB; PROTEIN YCF2; UNCLASSIFIED DRUG;

ARTICLE; CHLOROPLAST GENOME; CONTROLLED STUDY; CYTOPLASMIC MALE STERILITY; CYTOTYPE; DNA FLANKING REGION; DNA FRAGMENTATION; DNA POLYMORPHISM; EXON; GENE DISRUPTION; GENE INSERTION; GENETIC IDENTIFICATION; GENETIC ORGANIZATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; INTRON; MITOCHONDRIAL GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; ONION; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TRANS SPLICING;

BASE SEQUENCE; CHLOROPLASTS; CYTOPLASM; DNA; DNA, CHLOROPLAST; DNA, MITOCHONDRIAL; GENOME, CHLOROPLAST; GENOME, MITOCHONDRIAL; INTRONS; MITOCHONDRIA; ONIONS; OPEN READING FRAMES; TRANS-SPLICING;

ALLIUM CEPA;

EID: 77950867568     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-010-0290-6     Document Type: Article

References (56)

1. RV Abdelnoor R Yule A Elo AC Christensen G Meyer-Gauen SA Mackenzie 2003 Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS Proc Natl Acad Sci 100 5968 5973 10.1073/pnas.1037651100 1:CAS:528:DC%2BD3sXjvFOlt74%3D 12730382 (Pubitemid 36576915)
2. RV Abdelnoor AC Christensen S Mohammed B Munoz-Castillo H Moriyama SA Mackenzie 2006 Mitochondrial genome dynamics in plants and animals: convergent gene fusions of a MutS homologue J Mol Evol 63 165 173 10.1007/s00239-005-0226-9 1:CAS:528:DC%2BD28Xnt1yis70%3D 16830098 (Pubitemid 44126972)
3. B Albert B Godelle PH Gouyon 1998 Evolution of the plant mitochondrial genome: dynamics of duplication and deletion of sequences J Mol Evol 46 155 158 10.1007/PL00006290 1:CAS:528:DyaK1cXmslOgsg%3D%3D 9452517 (Pubitemid 28079939)
4. JO Allen CM Fauron P Mink L Roark S Oddiraju GN Lin L Meyer H Sun K Kim C Wang F Du D Xu M Gibson J Cifrese SW Clifton KJ Newton 2007 Comparisons among two fertile and three male-sterile mitochondrial genomes of maize Genetics 177 1173 1192 10.1534/genetics.107.073312 1:CAS:528:DC%2BD2sXhtlyrs7vL 17660568 (Pubitemid 350005664)
5. M Arrieta-Montiel A Lyznik M Woloszynska H Janska J Tohme S Mackenzie 2001 Tracing evolutionary and developmental implications of mitochondrial stoichiometric shifting in the common bean Genetics 158 851 864 1:CAS:528:DC%2BD3MXltFSisb0%3D 11404346 (Pubitemid 32552320)
6. S Backert BL Neilsen T Börner 1997 The mystery of the rings: structure and replication of mitochondrial genomes from higher plants Trend Plant Sci 2 477 483 10.1016/S1360-1385(97)01148-5 (Pubitemid 27518921)
7. M Bellaoui A Martin-Canadell G Pelletier F Budar 1998 Low-copy-number molecules are produced by recombination, actively maintained and can be amplified in the mitochondrial genome of Brassicaceae: relationship to reversion of the male sterile phenotype in some cybrids Mol Gen Genet 257 177 185 10.1007/s004380050637 1:CAS:528:DyaK1cXhsFyltLk%3D 9491076 (Pubitemid 28076072)
8. E Berninger 1965 Contribution à l'étude de la sterilité mâle de l'oignon (Allium cepa L.) Ann Amélior Plant 15 183 199
9. L Bonen 2008 Cis- and trans-splicing of group II introns in plant mitochondria Mitochondrion 8 26 34 10.1016/j.mito.2007.09.005 1:CAS:528:DC%2BD2sXhsVOlt77P 18006386 (Pubitemid 350263738)
10. F Budar P Touzet R De Paepe 2003 The nucleo-mitochondrial conflict in cytoplasmic male sterilities revised Genetica 117 3 16 10.1023/A:1022381016145 1:CAS:528:DC%2BD3sXhtFGjs70%3D 12656568 (Pubitemid 36352341)
11. J Castresana 2000 Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol Biol Evol 17 540 552 1:CAS:528:DC%2BD3cXisVSgt7g%3D 10742046 (Pubitemid 30210700)
12. T Engelke D Terefe T Tatlioglu 2003 A PCR-based marker system monitoring CMS-(S), CMS-(T) and (N)-cytoplasm in the onion (Allium cepa L.) Theor Appl Genet 107 162 167 1:CAS:528:DC%2BD3sXkvFyntLY%3D 12835941 (Pubitemid 36803505)
13. LM Gao M Möller XM Zhang ML Hollingsworth J Liu RR Mill M Gibby DZ Li 2007 High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam Mol Ecol 16 4684 4698 10.1111/j.1365-294X.2007.03537.x 1:CAS:528:DC%2BD1cXmsFahug%3D%3D 17908214 (Pubitemid 350135216)
14. S Glanz U Kück 2009 Trans-splicing of organelle introns-a detour to continuos RNAs Bioessays 31 921 934 10.1002/bies.200900036 1:CAS:528: DC%2BD1MXhtFOktLfO 19644921
15. TA Hall 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Window 95/98/NT Nucleic Acids Symp Ser 41 95 98 1:CAS:528:DC%2BD3cXhtVyjs7Y%3D
16. H Handa 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 10.1093/nar/gkg795 1:CAS:528:DC%2BD3sXotVCltr0%3D 14530439 (Pubitemid 37442317)
17. MR Hanson S Bentolila 2004 Interactions of mitochondrial and nuclear genes that affect male gametophyte development Plant Cell 16 S154 S169 10.1105/tpc.015966 1:CAS:528:DC%2BD2cXlsFWltb4%3D 15131248 (Pubitemid 38774225)
18. MJ Havey 1995 Identification of cytoplasms using the polymerase chain reaction to aid in the extraction of maintainer lines from open-pollinated populations of onion Theor Appl Genet 90 263 268 10.1007/BF00222212 1:CAS:528:DyaK2MXls1Cjs7Y%3D
19. MJ Havey 2000 Diversity among male-sterility-inducing and male-fertile cytoplasms of onion Theor Appl Genet 101 778 782 10.1007/s001220051543 1:CAS:528:DC%2BD3cXosFyhurk%3D
20. H Janska R Sarria M Woloszynska M Arrieta-Montiel SA Mackenzie 1998 Stoichiometric shifts in the common bean mitochondrial genome leading to male sterility and spontaneous reversion to fertility Plant Cell 10 1163 1180 10.1105/tpc.10.7.1163 1:CAS:528:DyaK1cXkvFejt7s%3D 9668135 (Pubitemid 28539999)
21. HA Jones A Clarke 1943 Inheritance of male sterility in the onion and the production of hybrid seed Proc Am Soc Hortic Sci 43 189 194
22. HA Jones SL Emsweller 1936 A male-sterile onion Proc Am Soc Hortic Sci 34 582 585
23. A Kanazawa N Tsutsumi A Hirai 1994 Reversible changes in the composition of the population of mtDNAs during dedifferentiation and regeneration in tobacco Genetics 138 865 870 1:CAS:528:DyaK28XitlKhsA%3D%3D 7851781 (Pubitemid 24337811)
24. S Kim H Lim S Park K Cho S Sung D Oh K Kim 2007 Identification of a novel mitochondrial genome type and development of molecular makers for cytoplasm classification in radish (Raphanus sativus L.) Theor Appl Genet 115 1137 1145 10.1007/s00122-007-0639-5 1:CAS:528:DC%2BD2sXht1aqt7bI 17828522 (Pubitemid 350043568)
25. S Kim E Lee DY Cho T Han H Bang BS Patil YK Ahn M Yoon 2009 Identification of a novel chimeric gene, orf725. and its use in development of a molecular marker for distinguishing among three cytoplasm types in onion (Allium cepa L.) Theor Appl Genet 118 433 441 10.1007/s00122-008-0909-x 1:CAS:528:DC%2BD1MXpt1Clsg%3D%3D 18936906
26. S Kim Y Lee H Lim Y Ahn S Sung 2009 Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.) Theor Appl Genet 119 189 198 10.1007/s00122-009-1028-z 1:CAS:528:DC%2BD1MXmslOktro%3D 19363601
27. B Kmiec M Woloszynska H Janska 2006 Heteroplasmy as a common state of mitochondrial genetic information in plants and animals Curr Genet 50 149 159 10.1007/s00294-006-0082-1 1:CAS:528:DC%2BD28XotFaltrw%3D 16763846 (Pubitemid 44227695)
28. V Knoop 2004 The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective Curr Genet 46 123 139 10.1007/s00294-004-0522-8 1:CAS:528:DC%2BD2cXntlSqsLc%3D 15300404 (Pubitemid 39307201)
29. T Kubo KJ Newton 2008 Angiosperm mitochondrial genomes and mutations Mitochondrion 8 5 14 10.1016/j.mito.2007.10.006 1:CAS:528:DC%2BD2sXhsVOlt77K 18065297 (Pubitemid 50009263)
30. cys(GCA) Nucleic Acids Res 28 2571 2576 10.1093/nar/28.13.2571 1:CAS:528:DC%2BD3cXlvFWqsLg%3D 10871408 (Pubitemid 30420856)
31. J Kudla FJ Albertazzi D Blazevic M Hermann R Bock 2002 Loss of the mitochondrial cox2 intron 1 in a family of monocotyledonous plants and utilization of mitochondrial intron sequences for the construction of a nuclear intron Mol Genet Genomics 267 223 230 10.1007/s00438-002-0657-6 1:CAS:528:DC%2BD38XkvVentbY%3D 11976966 (Pubitemid 34437998)
32. Y Lee S Park C Lim H Kim H Lim Y Ahn S Sung M Yoon S Kim 2008 Discovery of a novel cytoplasmic male-sterility and its restorer lines in radish (Raphanus sativus L.) Theor Appl Genet 117 905 913 10.1007/s00122-008-0830-3 18597066
33. SA Mackenzie CD Chase 1990 Fertility restoration is associated with loss of a portion of the mitochondrial genome in cytoplasmic male-sterile common bean Plant Cell 2 905 912 10.1105/tpc.2.9.905 1:CAS:528:DyaK3MXhtFKjtLs%3D 12354971
34. L Meng R Yang RJ Abbott G Miehe T Hu J Liu 2007 Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai-Tibetan plateau and adjacent highlands Mol Ecol 16 4128 4137 10.1111/j.1365-294X.2007.03459.x 1:CAS:528:DC%2BD2sXht1yhtLzL 17894761 (Pubitemid 47481047)
35. Y Notsu S Masood T Nishikawa N Kubo G Akiduki M Nakazono A Kirai K Kadowaki 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 10.1007/s00438-002-0767-1 1:CAS:528:DC%2BD38XptlWltb0%3D 12471441 (Pubitemid 35435847)
36. T Ohsako G Wang NT Miyashita 1996 Polymerase chain reaction-single strand conformational polymorphism analysis of intra- and interspecific variations in organellar DNA regions of Aegilops mutica and related species Genes Genet Syst 71 281 292 10.1266/ggs.71.281 1:CAS:528:DyaK2sXhsV2gu7c%3D 9037775 (Pubitemid 27039407)
37. DJ Oldenburg AJ Bendich 2001 Mitochondrial DNA from the Liverwort Marchantia polymorpha: circularly permuted linear molecules, head-to-tail concatemers, and a 5 protein J Mol Biol 310 549 562 10.1006/jmbi.2001.4783 1:CAS:528:DC%2BD3MXkvVOrsbw%3D 11439023 (Pubitemid 32692569)
38. JD Palmer 1988 Intraspecific variation and multicircularity in Brassica mitochondrial DNAs Genetics 118 341 351 1:CAS:528:DyaL1cXhs1Cqs70%3D 2834267
39. JD Palmer LA Herbon 1987 Unicircular structure of the Brassica hirta mitochondrial genome Curr Genet 11 565 570 10.1007/BF00384620 1:CAS:528:DyaL2sXhvFShs7Y%3D 2836082
40. AM Pyle O Fedorova C Waldsich 2007 Folding of group II introns: a model system for large, multidomain RNAs? Trend Biochem Sci 32 138 145 10.1016/j.tibs.2007.01.005 1:CAS:528:DC%2BD2sXisleisLc%3D 17289393 (Pubitemid 46367692)
41. Y Qiu JD Palmer 2004 Many independent origins of trans splicing of a plant mitochondrial group II intron J Mol Evol 59 80 89 1:CAS:528: DC%2BD2cXlsleisbg%3D 15383910 (Pubitemid 38858432)
42. X Reboud C Zeyl 1993 Organelle inheritance in plants Heredity 72 132 140 10.1038/hdy.1994.19 (Pubitemid 2048019)
43. T Sakai J Imamura 1993 Evidence for a mitochondrial sub-genome containing radish Atp1 in a Brassica napus cybrid Plant Sci 90 95 103 10.1016/0168- 9452(93)90160-2 1:CAS:528:DyaK3sXlslGitLo%3D
44. AS Sandhu RV Abdelnoor SA Mackenzie 2007 Transgenic induction of mitochondrial rearrangements for cytoplasmic male sterility in crop plants Proc Natl Acad Sci 104 1766 1770 10.1073/pnas.0609344104 1:CAS:528: DC%2BD2sXitVaqu74%3D 17261806 (Pubitemid 46239853)
45. Y Sato 1998 PCR amplification of CMS-specific mitochondrial nucleotide sequences to identify cytoplasmic genotypes of onion (Allium cepa L.) Theor Appl Genet 96 367 370 10.1007/s001220050750 1:CAS:528:DyaK1cXivVWls74%3D (Pubitemid 28178541)
46. M Satoh T Kubo S Nishizawa A Estiati N Itchoda T Mikami 2004 The cytoplasmic male-sterile type and normal type mitochondrial genomes of sugarbeet share the same complement of genes of known function but differ in the content of expressed ORFs Mol Gen Genomics 272 247 256 10.1007/s00438-004-1058-9 1:CAS:528:DC%2BD2cXos12isbk%3D (Pubitemid 39506559)
47. B Schweisguth 1973 Étude d'un nouveau type de sté rilité male chez l'oignon, Allium cepa L Ann Amélior Plant 23 221 233
48. V Shedge M Arrieta-Montiel AC Christensen SA Mackenzie 2007 Plant mitochondrial recombination surveillance requires unusual RecA and MutS homologs Plant Cell 19 1251 1264 10.1105/tpc.106.048355 1:CAS:528:DC%2BD2sXmsFelt7c%3D 17468263 (Pubitemid 46941652)
49. I Small R Suffolk CJ Leaver 1989 Evolution of plant mitochondrial genomes via substoichiometric intermediates Cell 58 69 76 10.1016/0092-8674(89)90403-0 1:CAS:528:DyaL1MXltFSisbo%3D 2752423
50. Y Sugiyama Y Watase M Nagase N Makita S Yagura A Hirai M Sugiura 2005 The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants Mol Gen Genomics 272 603 615 10.1007/s00438-004-1075-8 1:CAS:528:DC%2BD2MXhsVGks7c%3D (Pubitemid 40379316)
51. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol Biol Evol 24 1596 1599 10.1093/molbev/msm092 1:CAS:528:DC%2BD2sXpsVGrsL8%3D 17488738 (Pubitemid 47236692)
52. N Toor KS Keating SD Taylor AM Pyle 2008 Crystal structure of a self-spliced group II intron Science 320 77 82 10.1126/science.1153803 1:CAS:528:DC%2BD1cXktVKhtL8%3D 18388288 (Pubitemid 351490756)
53. M Unseld JR Marienfeld P Brandt A Brennicke 1997 The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366, 924 nucleotides Nature genet 15 57 61 10.1038/ng0197-57 1:CAS:528:DyaK2sXjsFSiuw%3D%3D 8988169 (Pubitemid 27014950)
54. BL Ward RS Anderson AJ Bendich 1981 The mitochondrial genome is large and variable in a family of plants (Cucurbitaceae) Cell 25 793 803 10.1016/0092-8674(81)90187-2 1:CAS:528:DyaL3MXls1Gkt7o%3D 6269758
55. M Woloszynska D Trojanowski 2009 Counting mtDNA molecules in Phaseolus vulgaaris: sublimons are constantly produced by recombination via short repeats and undergo rigorous selection during substoichiometric shifting Plant Mol Biol 70 511 521 10.1007/s11103-009-9488-8 1:CAS:528:DC%2BD1MXnt12nu78%3D 19387845
56. V Zaegel B Guermann M Le Ret C Andrés D Meyer M Erhardt J Canaday JM Gualberto P Imbault 2006 The plant-specific ssDNA binding protein OSB1 is involved in the stoichiometric transmission of mitochondrial DNA in Arabidopsis Plant Cell 18 3548 3563 10.1105/tpc.106.042028 1:CAS:528:DC%2BD2sXhvVKru78%3D 17189341 (Pubitemid 46464911)