Distribution of introns in the mitochondrial gene nad1 in land plants: Phylogenetic and molecular evolutionary implications

Molecular Phylogenetics and Evolution

Volumn 32, Issue 1, 2004, Pages 246-263

  Dombrovska, Olena ^a   Qiu, Yin Long ^a  

^a NONE

Author keywords

Genomic structural characters; Group II introns; Intron nomenclature; Land plant phylogeny; Mitochondrial DNA; nad1; RNA editing

Indexed keywords

MITOCHONDRIAL DNA; MITOCHONDRIAL PROTEIN; PRIMER DNA; VEGETABLE PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CONFORMATION; GENE; GENETIC VARIABILITY; GENETICS; GREEN ALGA; INTRON; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOSS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT; RNA EDITING; SEQUENCE HOMOLOGY; TIME;

ALGAE, GREEN; BASE SEQUENCE; BRYOPHYTA; DNA PRIMERS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, PLANT; INTRONS; MITOCHONDRIAL PROTEINS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLANT PROTEINS; PLANTS; RNA EDITING; SEQUENCE HOMOLOGY, NUCLEIC ACID; TIME FACTORS; VARIATION (GENETICS);

ADIANTUM; ALGAE; ANTHOCEROTOPHYTA; ASPLENIUM; BRYOPHYTA; CHLOROPHYTA; EMBRYOPHYTA; ENTOVALVA; EQUISETUM; HAPLOMITRIUM; ISOETES; LYCOPODIUM; MAGNOLIOPHYTA; MARATTIACEAE; MARCHANTIOPHYTA; MONILIFORMOPSES; OPHIOGLOSSUM; OSMUNDA; PTERIDOPHYTA; TRACHEOPHYTA;

EID: 3042698703     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.12.013     Document Type: Article

References (87)

1. Adams K.L., Qiu Y.-L., Stoutemyer M., Palmer J.D. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer during angiosperm evolution. Proc. Natl. Acad. Sci. USA. 99:2002;9905-9912
2. Anderberg A.A., Rydin C., Kallersjo M. Phylogenetic relationships in the order Ericales s.l.: analyses of molecular data from five genes from the plastid and mitochondrial genomes. Am. J. Bot. 89:2002;677-687
3. Beckert S., Muhle H., Pruchner D., Knoop V. The mitochondrial nad2 gene as a novel marker locus for phylogenetic analysis of early land plants: a comparative analysis in mosses. Mol. Phylogenet. Evol. 18:2001;117-126
4. Beckert S., Steinhauser S., Muhle H., Knoop V. A molecular phylogeny of bryophytes based on nucleotide sequences of the mitochondrial nad5 gene. Plant Syst. Evol. 218:1999;179-192
5. Chapdelaine Y., Bonen L. The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-in-pieces. Cell. 65:1991;465-472
6. Cho Y., Qiu Y.-L., Kuhlman P., Palmer J.D. Explosive invasion of plant mitochondria by a group I intron. Proc. Natl. Acad. Sci. USA. 95:1998;14244-14249
7. Conklin P.L., Wilson R.K., Hanson M.R. Multiple trans-splicing events are required to produce a mature nad1 transcript in a plant mitochondrion. Genes Dev. 5:1991;1407-1415
8. Crandall-Stotler B. Morphogenesis, developmental anatomy and bryophyte phylogenetics: contradictions of monophyly. J. Bryol. 14:1986;1-23
9. Denovan-Wright E.M., Nedelcu A.M., Lee R.W. Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos. Plant Mol. Biol. 36:1998;285-295
10. Douglas S., Zauner S., Fraunholz M., Beaton M., Penny S., Deng L.-T., Wu X., Reith M., Cavalier-Smith T., Maier U.-G. The highly reduced genome of an enslaved algal nucleus. Nature. 410:2001;1091-1096
11. Doyle J.J., Doyle J.S. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:1987;11-15
12. Edwards D., Duckett J.G., Richardson J.B. Hepatic characters in the earliest land plants. Nature. 374:1995;635-636
13. Gensel P.G., Edwards D. Plants Invade the Land: Evolutionary and Environmental Perspectives. 2001;Columbia University Press, New York, NY
14. Giege P., Brennicke A. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc. Natl. Acad. Sci. USA. 96:1999;15324-15329
15. Graham L.E. Origin of Land Plants. 1993;Wiley, New York, NY
16. Gugerli F., Sperisen C., Büchler U., Brunner I., Brodbeck S., Palmer J.D., Qiu Y.-L. The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny. Mol. Phylogenet. Evol. 21:2001;167-175
17. Hallick R.B., Hong L., Drager R.G., Favreau M.R., Monfort A., Orsat B., Spielmann A., Stutz E. Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res. 21:1993;3537-3544
18. Hashimoto K., Sato N. Characterization of the mitochondrial nad7 gene in Physcomitrella patens: similarity with angiosperm nad7 genes. Plant Sci. 160:2001;807-815
19. Hattori S., Inoue H. Preliminary report on Takakia lepidozioides. J. Hattori Bot. Lab. 19:1958;133-137
20. Hedderson T.A., Chapman R., Cox C.J. Bryophytes and the origins and diversification of land plants: new evidence from molecules. Bates J.W., Ashton N.W., Duckett J.G. Bryology for the Twenty-first Century. 1998;65-77 W.S. Maney & Son Ltd. Leeds, UK
21. Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C.-R., Meng B.-Y., Li Y.-Q., Kanno A., Nishizawa Y., Hirai A., Shinozaki K., Sugiura M. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217:1989;185-194
22. Johansen S., Haugen P. A new nomenclature of group I introns in ribosomal DNA. RNA. 7:2001;935-936
23. Joly S., Brouillet L., Bruneau A. Phylogenetic implications of the multiple losses of the mitochondrial coxII.i3 intron in the angiosperms. Int. J. Plant Sci. 162:2001;359-373
24. Kenrick P., Crane P.R. The origin and early evolution of plants on land. Nature. 389:1997;33-39
25. Kenrick P., Crane P.R. The Origin and Early Diversification of Land Plants: A Cladistic Study. 1997;Smithsonian Institution Press, Washington, DC
26. Kroymann J., Zetsche K. The mitochondrial genome of Chlorogonium elongatum inferred from the complete sequence. J. Mol. Evol. 47:1998;431-440
27. Cys (GCA). Nucleic Acids Res. 28:2000;2571-2576
28. Kück U., Jekosch K., Holzamer P. DNA sequence analysis of the complete mitochondrial genome of the green alga Scenedesmus obliquus: evidence for UAG being a leucine and UCA being a non-sense codon. Gene. 253:2000;13-18
29. Kudla J., Albertazzi F.J., Blazevic D., Hermann M., Bock R. 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. 267:2002;223-230
30. Kugita M., Kaneko A., Yamamoto Y., Takeya Y., Matsumoto T., Yoshinaga K. The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants. Nucleic Acids Res. 31:2003;716-721
31. Kugita M., Yamamoto Y., Fujikawa T., Matsumoto T., Yoshinaga K. RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res. 31:2003;2417-2423
32. Lambowitz A.M., Belfort M. Introns as mobile genetic elements. Annu. Rev. Biochem. 62:1993;587-622
33. Lewis L.A., Mishler B.D., Vilgalys R. Phylogenetic relationships of the liverworts (Hepaticae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL. Mol. Phylogenet. Evol. 7:1997;377-393
34. Malek O., Knoop V. Trans-splicing group II introns in plant mitochondria: the complete set of cis-arranged homologs in ferns, fern allies, and a hornwort. RNA. 4:1998;1599-1609
35. Malek O., Brennicke A., Knoop V. Evolution of trans-splicing plant mitochondrial introns in pre-Permian times. Proc. Natl. Acad. Sci. USA. 94:1997;553-558
36. Malek O., Lättig K., Hiesel R., Brennicke A., Knoop V. RNA editing in bryophytes and a molecular phylogeny of land plants. EMBO J. 15:1996;1403-1411
37. Manhart J.R., Palmer J.D. The gain of two chloroplast tRNA introns marks the green algal ancestors of land plants. Nature. 345:1990;268-270
38. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;911-940
39. Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns - a review. Gene. 82:1989;5-30
40. Mishler B.D., Lewis L.A., Buchheim M.A., Renzaglia K.S., Garbary D.J., Delwiche C.F., Zechman F.W., Kantz T.S., Chapman R.L. Phylogenetic relationships of the "green algae" and "bryophytes" Ann. Missouri Bot. Gard. 81:1994;451-483
41. Mizutani M. A new knowledge of archegonia of Takakia lepidozioides. J. Jpn. Bot. 42:1967;379-381
42. Mohr G., Perlman P.S., Lambowitz A.M. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Res. 21:1993;4991-4997
43. Nakayama H., Morinaga Y., Nomura N., Nunoura T., Sako Y., Uchida A. An archaeal homing endonuclease I-Pog I cleaves at the insertion site of the neighboring intron, which has no nested open reading frame. FEBS. 544:2003;165-170
44. Nedelcu A.M., Lee R.W., Lemieux C., Gray M.W., 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. 10:2000;819-831
45. Newton A.E., Cox C.J., Duckett J.G., Wheeler J.A., Goffinet B., Hedderson T.A.J., Mishler B.D. Evolution of major moss lineages: phylogenetic analyses based on multiple gene sequences and morphology. Bryologist. 103:2000;187-211
46. Nickrent D.L., Parkinson C.L., Palmer J.D., Duff R.J. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol. Biol. Evol. 17:2000;1885-1895
47. Nishiyama T., Kato M. Molecular phylogenetic analysis among bryophytes and tracheophytes based on combined data of plastid coded genes and the 18S rRNA gene. Mol. Biol. Evol. 16:1999;1027-1036
48. 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. 268:2002;434-445
49. 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: a primitive form of plant mitochondrial genome. J. Mol. Biol. 223:1992;1-7
50. Ohyama K., Fukuzawa H., Kohchi T., Shirai H., Sano T., Sano S., Umesono K., Shiki Y., Takeuchi M., Chang Z., Aota S., Inokuchi H., Ozeki H. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature. 322:1986;572-574
51. Pruchner D., Beckert S., Muhle H., Knoop V. Divergent intron conservation in the mitochondrial nad2 gene: signatures for the three bryophyte classes (mosses, liverworts, and hornworts) and the lycophytes. J. Mol. Evol. 55:2002;265-271
52. Pruchner D., Nassal B., Schindler M., Knoop V. Mosses share mitochondrial group II introns with flowering plants, not with liverworts. Mol. Genet. Genomics. 266:2001;608-613
53. Pryer K.M., Schneider H., Smith A.R., Cranfill R., Wolf P.G., Hunt J.S., Sipes S.D. Horsetails and ferns are a monophyletic group and the closest relatives to seed plants. Nature. 409:2001;618-622
54. Qin P.Z., Pyle A.M. The architectural organization and mechanistic function of group II intron structural elements. Curr. Opin. Struct. Biol. 8:1998;301-308
55. Qiu Y.-L., Cho Y., Cox J.C., Palmer J.D. The gain of three mitochondrial introns identifies liverworts as the earliest land plants. Nature. 394:1998;671-674
56. Qiu Y.-L., Lee J., Bernasconi-Quadroni F., Soltis D.E., Soltis P.S., Zanis M., Zimmer E.A., Chen Z., Savolainen V., Chase M.W. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature. 402:1999;404-407
57. Qiu Y.-L., Lee J. Transition to a land flora: a molecular phylogenetic perspective. J. Phycol. 36:2000;799-802
58. Qiu, Y.-L., Palmer, J.D., in press. Many independent origins of trans-splicing of a plant mitochondrial group II intron. J. Mol. Evol.
59. Rabbi M.F., Wilson K.G. The mitochondrial coxII intron has been lost in two different lineages of dicots and altered in others. Am. J. Bot. 80:1993;1216-1223
60. Raubeson L.A., Jansen R.K. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science. 255:1992;1697-1699
61. Renzaglia K.S., Duff R.J., Nickrent D.L., Garbary D.J. Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny. Philos. Trans. R. Soc. B. 355:2000;769-793
62. Samigullin T.K., Yacentyuk S.P., Degtyaryeva G.V., Valiehoroman K.M., Bobrova V.K., Capesius I., Martin W.M., Troitsky A.V., Filin V.R., Antonov A.S. Paraphyly of bryophytes and close relationship of hornworts and vascular plants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences. Arctoa. 11:2002;31-43
63. Schuster R.M. The Hepaticae and Anthocerotae of North America, vol. 1. 1966;Columbia University Press, New York, NY
64. Schuster, R.M., 2000. Austral Hepaticae, Part I. J. Cramer in der Gebrueder Borntraeger Verlagsbuchhandlung, Stuttgart
65. Sharp P.A. Speculations on RNA splicing. Cell. 23:1981;643-646
66. Smith D.K., Davison P.G. Antheridia and sporophytes in Takakia ceratophylla (Mitt.) Grolle: evidence for reclassification among the mosses. J. Hattori Bot. Lab. 73:1993;263-271
67. Steinhauser S., Beckert S., Capesius I., Malek O., Knoop V. Plant mitochondrial RNA editing. J. Mol. Evol. 48:1999;303-312
68. Sugiura C., Kobayashi Y., Aoki S., Sugita C., Sugita M. Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Res. 31:2003;5324-5331
69. Swofford D.L. PAUP*4.0b10: Phylogenetic analysis using parsimony. 2003;Sinauer, Sunderland, MA
70. Taylor W.A. Spores in earliest land plants. Nature. 373:1995;391-392
71. Thomson M.C., MacFarlane J.L., Beagley C.T., Wolstenholme D.R. RNA editing of mat-r transcripts in maize and soybean increases similarity of the encoded protein to fungal and bryophyte group II intron maturases: evidence that mat-r encodes a functional protein. Nucleic Acids Res. 22:1994;5745-5752
72. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:1997;4876-4882
73. Turmel M., Lemieux C., Burger G., Lang B.F., Otis C., Plante I., Gray M.W. The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor: two radically different evolutionary patterns within green algae. Plant Cell. 11:1999;1717-1729
74. 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 a highly compact mitochondrial genome in the ancestor of all green plants. Mol. Biol. Evol. 19:2002;24-38
75. 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 linegae that led to land plants. Proc. Natl. Acad. Sci. USA. 99:2002;11275-11280
76. 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. 15:2003;1888-1903
77. Unseld M., Marienfeld J.R., Brand P., Brennicke A. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366, 924 nucleotides. Nat. Genet. 15:1997;57-61
78. Vangerow S., Teekorn T., Knoop V. Phylogenetic information in the mitochondrial nad5 gene of pteridophytes: RNA editing and intron sequences. Plant Biol. 1:1999;235-243
79. Wakasugi T., Sugita M., Tsudzuki T., Sugiura M. Updated gene map of tobacco chloroplast DNA. Plant Mol. Biol. Rep. 16:1998;231-241
80. Wahleithner J.A., MacFarlane J.L., Wolstenholme D.R. A sequence encoding a maturase-related protein in a group II intron of a plant mitochondrial nad1 gene. Proc. Natl. Acad. Sci. USA. 87:1990;548-552
81. Wellman C.H., Osterloff P.L., Mohiuddin U. Fragments of the earliest land plants. Nature. 425:2003;282-285
82. Wissinger B., Schuster W., Brennicke A. Trans-splicing in Oenothera mitochondria: nad1 mRNA are edited in exon and trans-splicing group II intron sequences. Cell. 65:1991;473-482
83. Wolf P.G., Rowe C.A., Sinclair R.B., Hasebe M. Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Res. 10:2003;59-65
84. Wolff G., Plante I., Lang B.F., Kück U., Burger G. Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii: gene content and genome organization. J. Mol. Biol. 237:1994;75-86
85. Won H., Renner S.S. Horizontal gene transfer from flowering plants to Gnetum. Proc. Natl. Acad. Sci. USA. 100:2003;10824-10829
86. Zimmerly S., Hausner G., Wu X.-C. Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res. 29:2001;1238-1250
87. Zuker M., Mathews D.H., Turner D.H. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. Barciszewski J., Clark B.F.C. RNA Biochemistry and Biotechnology. NATO ASI Series. 1999;11-43 Kluwer Academic Publishers, Dordrecht