Extensive intraindividual variation in plastid rDNA sequences from the Holoparasite Cynomorium coccineum (Cynomoriaceae)

Journal of Molecular Evolution

Volumn 58, Issue 3, 2004, Pages 322-332

  García, Miguel A ^a   Nicholson, Erica H ^b   Nickrent, Daniel L ^b  

^a CSIC   (Spain)

^b SOUTHERN ILLINOIS UNIVERSITY   (United States)

Author keywords

23S rRNA; Chloroplast; Heteroplasmy; Nonphotosynthetic; Ribosomal RNA; RNA structural model

Indexed keywords

RIBOSOME DNA;

ARTICLE; CELL NUCLEUS; CISTRON; CYNOMORIUM COCCINEUM; DNA SEQUENCE; GENE AMPLIFICATION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC COMPLEMENTATION; GENETIC CONSERVATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HETEROPLASMY; INDIVIDUALITY; MITOCHONDRION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITE; PHOTOSYNTHESIS; PLASTID; POLYMERASE CHAIN REACTION; PROTEIN PURIFICATION; TAXONOMY;

BASE COMPOSITION; BASE PAIRING; BASE SEQUENCE; CYNOMORIUM; DNA PRIMERS; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; PLASTIDS; SEQUENCE ANALYSIS, DNA; SPAIN; VARIATION (GENETICS);

ALGAE; CHLOROPHYTA; CYNOMORIACEAE; CYNOMORIUM; CYNOMORIUM COCCINEUM; MAGNOLIOPHYTA; TRACHEOPHYTA;

EID: 1842427217     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2554-y     Document Type: Article

References (37)

1. Bakker FT, Culham A, Gómez-Martínez R, Carvalho J, Compton J, Dawtrey R Gibby M (2000) Patterns of nucleotide substitution in angiosperm cpDNA trnL (UAA)-trnF (GAA) regions. Mol Biol Evol 17:1146-1155
2. Börner T, Sears BB (1986) Plastome mutants. Plant Mol Biol Report 4:69-92
3. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR (2002) The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BioMed Central Bioinform 3:2
4. Chat J, Decroocq S, Decroocq V, Petit RJ (2002) A case of chloroplast heteroplasmy in kiwifruit (Actinidia deliciosa) that is not transmitted during sexual reproduction. J Hered 93:293-300
5. Chesser RK (1998) Heteroplasmy and organelle gene dynamics. Genetics 150:1309-1327
6. Chinnery PF, Thorburn DR, Samuels DC, White SL, Dahl HHM, Turnbull DM, Lightowlers RN, Howell N (2000) The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both. Trends. Genet 16:500-505
7. Cummings MP, Nugent JM, Olmstead RG, Palmer JD (2003) Phylogenetic analysis reveals five independent transfers of the chloroplast gen rbcL to the mitochondrial genome in angiosperms. Curr Genet 43:131-138
8. Duff RJ, Nickrent DL (1997) Characterization of mithocondrial small-subunit ribosomal RNAs from holoparasitic plants. J Mol Evol 45:631-639
9. Frey JE (1999) Genetic flexibility of plant chloroplasts. Nature 398:115-116
10. Frey JE, Müller-Schärer H, Frey B, Frey D (1999) Complex relation between triazine-susceptible phenotype and genotype in the weed Senecio vulgaris may be caused by chloroplast DNA polymorphism. Theor Appl Genet 99:578-586
11. Gillham NW, Boynton JE, Harris EH (1991) Transmission of plastid genes. In: Bogorad L, Vasil IK (eds) The molecular biology of plastids. Academic Press, London/New York, pp, 55-92
12. Goodman, MF (1997) Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity. Proc Natl Acad Sci USA 94:10493-10495
13. Gutell RR, Lee JC, Cannone JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12:301-310
14. Harada T, Sato T, Asaka D, Mitsukawa I (1991) Large-scale deletions of rice plastid DNA in anther culture. Theor Appl Genet 81:157-161
15. Hattori N, Kitagawa K, Takumi S, Nakamura C (2002) Mitochondrial DNA heteroplasmy in wheat, Aegilops and their nucleus-cytoplasm hybrids. Genetics 160:1619-1630
16. Johnson LB, Palmer JD (1989) Heteroplasmy of chloroplast DNA in Medicago. Plant Mol Biol 12:3-11
17. Lax AR, Vaughn KC, Duke SO, Endrizzi JE (1987) Structural and physiological studies of a plastome cotton mutant with slow sorting out. J Hered 78:147-152
18. Lee DJ, Blake TK, Smith SE (1988) Biparental inheritance of chloroplast DNA and the existence of heteroplasmic cells in alfalfa. Theor Appl Genet 76:545-549
19. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 99:12246-12251
20. Miyata S, Nakazono M, Hirai A (1998) Transcription of plastid-derived tRNA genes in rice mitochondria. Curr Genet 34:216-220
21. Nakazono M, Hirai A (1993) Identification of the entire set of transferred chloroplast sequences in the mitochondrial genome of rice. Mol Gen. Genet. 236:341-346
22. Nedelcu AM (2001) Complex patterns of plastid 16S rRNA gene evolution in nonphotosynthetic green algae. J Mol Evol 53:670-679
23. Nickrent DL (1994) From field to film: rapid sequencing methods for field collected plant species. BioTechniques 16:470-475
24. Nickrent DL, Duff RJ, Konings DAM (1997a) Structural analyses of plastid-derived 16S rRNAs in holoparasitic angiosperms. Plant Mol Biol 34:731-743
25. Nickrent DL, Ouyang Y, Duff RJ, dePamphilis C (1997b) Do nonasterid holoparasites flowering plants have plastid genomes? Plant Mol Biol 34:717-729
26. Rambaut A (1996) Se-Al Sequence Alignment Editor. Department of Zoology, University of Oxford
27. Rand DM (2001) The units of selection on mitochondrial DNA. Annu Rev Ecol 32:415-448
28. Rousset F, Pelandakis M, Solignac M (1991) Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA. Proc Natl Acad Sci USA 88:10032-10036
29. Schnare NM, Damberger SH, Gray MW, Gutell RR (1996) Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA. J Mol Biol 256:701-719
30. Severi A, Laudi G, Fornasiero RB (1980) Ultrastructural researches in the plastids of parasitic plants. VI. Scales of Cytinus hypocistis L. Caryologia 33:307-313
31. Springer MS, Hollar LJ, Burk A (1995) Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals. Mol Biol Evol 12:1138-1150
32. Städler T, Delph LF (2002) Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant. Proc Natl Acad Sci USA 99:11730-11735
33. Stern DB, Lonsdale DM (1982) Mitochondrial and chloroplast genomes of maize have 12-kilobase DNA sequence in common. Nature 299:698-702
34. Vernon D, Gutell RR, Cannone JJ, Rumpf RW, Birky Jr CW (2001) Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma. Mol Biol Evol 18:1810-1822
35. Yamagishi M (2002) Heterogeneous plastid genomes in anther culture-derived albino rice plants. Euphytica 123:67-74
36. Young D, dePamphilis C (2000) Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants. Mol Biol Evol 17:1933-1941
37. Zubko MK, Day A (1998) Stable albinism induced without mutagenesis: a model for ribosome-free plastid inheritance. Plant J 15:265-271