An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Turmel, Monique ^a   Otis, Christian ^a   Lemieux, Claude ^a  

^a UNIVERSITÉ LAVAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; CHAETOSPHAERIDIUM; CHARA; CHAROPHYTA; CHLOROKYBUS ATMOPHYTICUS; CONTROLLED STUDY; DNA SEQUENCE; GENE CLUSTER; GENE MAPPING; GENE ORDER; GENETIC LINKAGE; GREEN ALGA; INTRON; MARCHANTIA; MARCHANTIA POLYMORPHA; MITOCHONDRIAL GENETICS; MOSS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYSCOMITRELLA; PHYSCOMITRELLA PATENS; STREPTOPHYTA; CHROMOSOME MAP; COMPARATIVE STUDY; DNA PACKAGING; GENETICS; GENOME; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; TANDEM REPEAT;

BRYOPHYTES; CHAETOSPHAERIDIUM; CHARA; CHAROPHYCEAE; CHLOROKYBALES; CHLOROKYBUS; CHLOROKYBUS ATMOPHYTICUS; CHLOROPHYTA; EMBRYOPHYTA; MARCHANTIA POLYMORPHA; MESOSTIGMA; MESOSTIGMA VIRIDE; MESOSTIGMATALES; PHYSCOMITRELLA PATENS; STREPTOPHYTA;

ALGAE, GREEN; BASE SEQUENCE; CHROMOSOME MAPPING; DNA PACKAGING; DNA, MITOCHONDRIAL; GENOME; INTRONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; TANDEM REPEAT SEQUENCES;

EID: 34347235160     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-137     Document Type: Article

References (69)

1. Graham LE Cook ME Busse JS The origin of plants: Body plan changes contributing to a major evolutionary radiation Proc Natl Acad Sci USA 2000 97 4535-4540 34322 10781058 10.1073/pnas.97.9.4535
2. Lewis LA McCourt RM Green algae and the origin of land plants Am J Bot 2004 91 10 1535-1556
3. Bremer K Humphries CJ Mishler BD Churchill SP On cladistic relationships in green plants Taxon 1987 36 339-349 10.2307/1221429
4. Karol KG McCourt RM Cimino MT Delwiche CF The closest living relatives of land plants Science 2001 294 5550 2351-2353 10.1126/science.1065156 11743201
5. Melkonian M Phylum Chlorophyta. Class Prasinophyceae Handbook of Protoctista The Structure, Cultivation, Habitats and Life Histories of the Eukaryotic Microorganisms and their Descendants Exclusive of Animals, Plants and Fungi Boston, Jones and Bartlett Publishers Margulis L, Corliss JO, Melkonian M, Chapman DJ 1990 600-607
6. Mattox KR Stewart KD Classification of the green algae: A concept based on comparative cytology The Systematics of the Green Algae London, Academic Press Irvine DEG, John DM 1984 29-72
7. McCourt RM Delwiche CF Karol KG Charophyte algae and land plant origins Trends Ecol Evol 2004 19 661-666 10.1016/j.tree.2004.09.013 16701329
8. Lemieux C Otis C Turmel M Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution Nature 2000 403 6770 649-652 10.1038/35001059 10688199
9. Turmel M Ehara M Otis C Lemieux C Phylogenetic relationships among streptophytes as inferred from chloroplast small and large subunit rRNA gene sequences J Phycol 2002 38 364-375 10.1046/j.1529-8817.2002.01163.x
10. Turmel M Otis C Lemieux C The complete mitochondrial DNA sequence of Mesostigma viride identifies this green alga as the earliest green plant divergence and predicts a highly compact mitochondrial genome in the ancestor of all green plants Mol Biol Evol 2002 19 1 24-38 11752187
11. Turmel M Otis C Lemieux C The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants Mol Biol Evol 2006 23 6 1324-1338 10.1093/molbev/msk018 16611644
12. Turmel M Pombert JF Charlebois P Otis C Lemieux C The green algal ancestry of land plants as revealed by the chloroplast genome Int J Plant Sci 2007 168 5 679-689 10.1086/513470
13. Lemieux C Otis C Turmel M A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies BMC Biol 2007 5 2 1781420 17222354 10.1186/1741-7007-5-2
14. Rodriguez-Ezpeleta N Philippe H Brinkmann H Becker B Melkonian M Phylogenetic analyses of nuclear, mitochondrial and plastid multi-gene datasets support the placement of Mesostigma in the Streptophyta Mol Biol Evol 2007 24 3 723-731 10.1093/molbev/msl200 17172635
15. Marin B Melkonian M Mesostigmatophyceae, a new class of streptophyte green algae revealed by SSU rRNA sequence comparisons Protist 1999 150 4 399-417 10714774
16. Bhattacharya D Weber K An SS Berning-Koch W Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants J Mol Evol 1998 47 544-550 10.1007/PL00006410 9797404
17. Martin W Deusch O Stawski N Grunheit N Goremykin V Chloroplast genome phylogenetics: Why we need independent approaches to plant molecular evolution Trends Plant Sci 2005 10 203-209 10.1016/j.tplants.2005.03.007 15882651
18. Rogers MB Gilson PR Su V McFadden GI Keeling PJ The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: Evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts Mol Biol Evol 2007 24 1 54-62 10.1093/molbev/msl129 16990439
19. Turmel M Otis C Lemieux C The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants Proc Natl Acad Sci USA 2002 99 17 11275-11280 123247 12161560 10.1073/pnas.162203299
20. Turmel M Otis C Lemieux C The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants Plant Cell 2003 15 1888-1903 167177 12897260 10.1105/tpc.013169
21. Oda K Yamato K Ohta E Nakamura Y Takemura M Nozato N Akashi K Kanegae T Ogura Y Kohchi T Ohyama K Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA J Mol Biol 1992 223 1-7 10.1016/0022-2836(92)90708-R 1731062
22. Terasawa K Odahara M Kabeya Y Kikugawa T Sekine Y Fujiwara M Sato N The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants Mol Biol Evol 2007 24 3 699-709 10.1093/molbev/msl198 17175527
23. 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 2003 31 20 5907-5916 219474 14530439 10.1093/ nar/gkg795
24. Kubo T Nishizawa S Sugawara A Itchoda N Estiati A Mikami T The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA) Nucleic Acids Res 2000 28 13 2571-2576 102699 10871408 10.1093/nar/28.13.2571
25. Notsu Y Masood S Nishikawa T Kubo N Akiduki G Nakazono M Hirai A 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 2002 268 434-445 10.1007/s00438-002-0767-1 12471441
26. Sugiyama Y Watase Y Nagase M Makita N Yagura S Hirai A 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 2005 272 6 603-615 10.1007/ s00438-004-1075-8 15583938
27. Unseld M Marienfeld JR Brandt P Brennicke A The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides Nat Genet 1997 15 57-61 10.1038/ng0197-57 8988169
28. Clifton SW Minx P Fauron CM Gibson M Allen JO Sun H Thompson M Barbazuk WB Kanuganti S Tayloe C Meyer L Wilson RK Newton KJ Sequence and comparative analysis of the maize NB mitochondrial genome Plant physiology 2004 136 3 3486-3503 527149 15542500 10.1104/pp.104.044602
29. Ogihara Y Yamazaki Y Murai K Kanno A Terachi T Shiina T Miyashita N Nasuda S Nakamura C Mori N Takumi S Murata M Futo S Tsunewaki K Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome Nucleic Acids Res 2005 33 19 6235-6250 1275586 16260473 10.1093/nar/gki925
30. Turmel M Lemieux C Burger G Lang BF Otis C Plante I Gray MW The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor: Two radically different evolutionary patterns within green algae Plant Cell 1999 11 9 1717-1729 144307 10488238 10.1105/tpc.11.9.1717
31. Pombert JF Beauchamp P Otis C Lemieux C Turmel M The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae Curr Genet 2006 50 2 137-147 10.1007/s00294-006-0076-z 16721603
32. Robbens S Derelle E Ferraz C Wuyts J Moreau H Van de Peer Y The complete chloroplast and mitochondrial DNA sequences of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction Mol Biol Evol 2007 24 4 956-968 10.1093/molbev/msm012 17251180
33. Hauth AM Maier UG Lang BF Burger G The Rhodomonas salina mitochondrial genome: Bacteria-like operons, compact gene arrangement and complex repeat region Nucleic Acids Res 2005 33 14 4433-4442 1183108 16085754 10.1093/nar/gki757
34. Ma DP King YT Kim Y Luckett WS Jr. The group I intron of apocytochrome b gene from Chlamydomonas smithii encodes a site-specific endonuclease Plant Mol Biol 1992 18 5 1001-1004 10.1007/BF00019218 1316190
35. Thompson AJ Yuan X Kudlicki W Herrin DL Cleavage and recognition pattern of a double-strand-specific endonuclease (I-CreI) encoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii Gene 1992 119 2 247-251 10.1016/0378-1119(92)90278-W 1398106
36. Turmel M Mercier JP Côté V Otis C Lemieux C The site-specific DNA endonuclease encoded by a group I intron in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene introduces a single-strand break at low concentrations of Mg2+ Nucleic Acids Res 1995 23 2519-2525 307060 7630730 10.1093/nar/23.13.2519
37. Wolff G Plante I Lang BF Kück U Burger G Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii J Mol Biol 1994 237 75-86 10.1006/jmbi.1994.1210 8133522
38. Lang BF Burger G O'Kelly CJ Cedergren R Golding GB Lemieux C Sankoff D Turmel M Gray MW An ancestral mitochondrial DNA resembling a eubacterial genome in miniature Nature 1997 387 6632 493-497 10.1038/387493a0 9168110
39. Denovan-Wright EM Nedelcu AM Lee RW Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos Plant Mol Biol 1998 36 2 285-295 10.1023/A:1005995718091 9484440
40. Pombert JF Otis C Lemieux C Turmel M The complete mitochondrial DNA sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) highlights distinctive evolutionary trends in the Chlorophyta and suggests a sister-group relationship between the Ulvophyceae and Chlorophyceae Mol Biol Evol 2004 21 5 922-935 10.1093/molbev/msh099 15014170
41. Cho Y Qiu YL Kuhlman P Palmer JD Explosive invasion of plant mitochondria by a group I intron Proc Natl Acad Sci USA 1998 95 24 14244-14249 24358 9826685 10.1073/pnas.95.24.14244
42. Fontaine JM Goux D Kloareg B Loiseaux-de Goër S The reverse-transcriptase-like proteins encoded by group II introns in the mitochondrial genome of the brown alga Pylaiella littoralis belong to two different lineages which apparently coevolved with the group II ribozyme lineages. J Mol Evol 1997 44 33-42 10.1007/PL00006119 9010134
43. Felsenstein J Inferring phylogenies Sunderland (MA), Sinauer Associates Inc 2004 266 418-427
44. Knoop V The mitochondrial DNA of land plants: Peculiarities in phylogenetic perspective Curr Genet 2004 46 3 123-139 10.1007/ s00294-004-0522-8 15300404
45. Nedelcu AM Lee RW Lemieux C Gray MW Burger G The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome Genome Res 2000 10 819-831 310893 10854413 10.1101/gr.10.6.819
46. Burger G Saint-Louis D Gray MW Lang BF Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea: Cyanobacterial introns and shared ancestry of red and green algae Plant Cell 1999 11 1675-1694 144311 10488235 10.1105/tpc.11.9.1675
47. Leblanc C Boyen C Richard O Bonnard G Grienenberger JM Kloareg B Complete sequence of the mitochondrial DNA of the rhodophyte Chondrus crispus (Gigartinales): Gene content and genome organization J Mol Biol 1995 250 484-495 10.1006/jmbi.1995.0392 7616569
48. Ohta N Sato N Kuroiwa T Structure and organization of the mitochondrial genome of the unicellular red alga Cyanidioschyzon merolae deduced from the complete nucleotide sequence Nucleic Acids Res 1998 26 5190-5198 147977 9801318 10.1093/nar/26.22.5190
49. Oudot-Le Secq MP Kloareg B Loiseaux-De GO Euml R S The mitochondrial genome of the brown alga Laminaria digitata: A comparative analysis Eur J Phycol 2002 37 02 163-172 10.1017/S0967026202003542
50. Gray MW Lang BF Burger G Mitochondria of protists Annu Rev Genet 2004 38 477-524 10.1146/annurev.genet.37.110801.142526 15568984
51. Palmer JD Plastid chromosomes: Structure and evolution The Molecular Biology of Plastids San Diego, Academic Press Bogorad L, Vasil K 1991 5-53
52. Boer PH Gray MW Short dispersed repeats localized in spacer regions in Chlamydomonas reinhardtii mitochondrial DNA Curr Genet 1991 19 309-312 10.1007/BF00355060 1831072
53. Kroymann J Zetsche K The mitochondrial genome of Chlorogonium elongatum inferred from the complete sequence J Mol Evol 1998 47 431-440 10.1007/ PL00006400 9767688
54. Vahrenholz C Rieman G Pratje E Dujon B Michaelis G Mitochondrial DNA of Chlamydomonas reinhardtii: The structure of the ends of the linear 15.8-kb genome suggests mechanisms for DNA replication Curr Genet 1993 24 241-247 10.1007/BF00351798 8221933
55. Andersen RA Berges JA Harrison PJ Watanabe MM Appendix A-Recipes for freshwater and seawater media Algal Culturing Techniques Burlington, Elsevier Academic Press Andersen RA 2005 429-538
56. Turmel M Otis C Lemieux C The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales BMC Biology 2005 3 22 1277820 16236178 10.1186/ 1741-7007-3-22
57. Pombert JF Otis C Lemieux C Turmel M The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages Mol Biol Evol 2005 22 9 1903-1918 10.1093/molbev/ msi182 15930151
58. Michel F Westhof E Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis J Mol Biol 1990 216 3 585-610 10.1016/0022-2836(90)90386-Z 2258934
59. Michel F Umesono K Ozeki H Comparative and functional anatomy of group II catalytic introns - a review Gene 1989 82 1 5-30 10.1016/ 0378-1119(89)90026-7 2684776
60. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990 215 403-410 2231712
61. Kurtz S Choudhuri JV Ohlebusch E Schleiermacher C Stoye J Giegerich R REPuter: The manifold applications of repeat analysis on a genomic scale Nucleic Acids Res 2001 29 22 4633-4642 92531 11713313 10.1093/nar/ 29.22.4633
62. Comparative Repeat Analysis http://bugmaster.jgi-psf.org/repeats/
63. Rice P Longden I Bleasby A EMBOSS: The European Molecular Biology Open Software Suite Trends Genet 2000 16 6 276-277 10.1016/ S0168-9525(00)02024-2 10827456
64. RepeatMasker http://www.repeatmasker.org/
65. WU-BLAST http://blast.wustl.edu/
66. Tesler G GRIMM: Genome rearrangements web server Bioinformatics 2002 18 492-493 10.1093/bioinformatics/18.3.492 11934753
67. Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 2003 52 5 696-704 10.1080/10635150390235520 14530136
68. Felsenstein J PHYLIP (phylogeny inference package). Version 3.5 Department of Genetics, University of Washington, Seattle, Distributed by the author 1995
69. Swofford DL PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4 Sunderland, Massachusetts, Sinauer Associates 2003