Hairpins create minute inversions in non coding regions of chloroplast DNA

Current Genetics

Volumn 30, Issue 3, 1996, Pages 259-262

  Kelchner, Scot A ^a   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Inversions; Molecular evolution; Non coding DNA; Phylogenetics; rpl16 intron

Indexed keywords

CHLOROPLAST DNA;

ARTICLE; CHROMOSOME INVERSION; COMPARATIVE STUDY; DNA STRUCTURE; HIGHER PLANT; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

BASE SEQUENCE; CHLOROPLASTS; DNA, PLANT; EXONS; GENES, PLANT; INTRONS; INVERSION, CHROMOSOME; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLANTS; POLYMORPHISM, GENETIC;

BAMBUSA; CHUSQUEA; EMBRYOPHYTA; POACEAE;

EID: 0029811392     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002940050130     Document Type: Article

References (27)

1. Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ (1995) The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann Missouri Bot Gard 82:247-277
2. Clark LG, Zhang W, Wendel JF (1995) A phylogeny of the grass family (Poaceae) based on ndhF sequence data. Syst Bot 20:436-460
3. Dixon MT, Hillis DM (1993) Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10:256-267
4. Downie SR, Palmer JD (1992) Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In: Soltis DE et al. (eds) Molecular systematics of plants. Chapman and Hall, New York, pp 14-35
5. Downie SR, Palmer JD (1994) A chloroplast DNA phylogeny of the Caryophyllales based on structural and inverted repeat restriction-site variation. Syst Bot 19:236-252
6. Ferris C, Oliver RP, Davy AJ, Hewitt GM (1995) Using chloroplast DNA to trace postglacial migration routes of oaks into Britain. Mol Ecol 4:731-738
7. Gielly L, Taberlet P (1994) The use of chloroplast DNA to resolve plant phylogenies: non-coding versus rbcL sequences. Mol Biol Evol 11:769-777
8. Golenberg EM, Clegg MT, Durbin ML, Doebley J, Ma DP (1993) Evolution of a non-coding region of the chloroplast genome. Mol Phyl Evol 2:52-64
9. Hong YP, Hipkins VD, Strauss SH (1993) Chloroplast DNA diversity among trees, populations and species in the California closed-cone pines (Pinus rudiata, Pinus muricata, and Pinus attenuata). Genetics 135:1187-1196
10. Hoot SB, Palmer JD (1994) Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera. J Mol Evol 38:274-281
11. Howe CJ (1985) The endpoints of an inversion in wheat chloroplast DNA are associated with short repeated sequences containing homology to att-lambda. Curr Genet 10:139-145
12. Johnson LA, Soltis DE (1994) matK DNA sequences and phylogenetic reconstruction in Saxifragaceae s. str. Syst Bot 19:143-156
13. Kanno A, Hirai A (1992) Comparative studies of the structure of chloroplast DNA from four species of Oryza: cloning and physical maps. Theor Appl Genet 83:791-798
14. Kanno A, Watanabe N, Nakamura I, Hirai A (1993) Variations in chloroplast DNA from rice (Oryza sativa): differences between deletions mediated by short direct-repeat sequences within a single species. Theor Appl Genet 86:579-584
15. Knox EB, Downie SR, Palmer JD (1993) Chloroplast genome rearrangements and the evolution of giant lobelias from herbaceous ancestors. Mol Biol Evol 10:414-430
16. Milligan BG, Hampton JN, Palmer JD (1989) Dispersed repeats and structural reorganization in subclover chloroplast DNA. Mol Biol Evol 6:355-368
17. Morton BR, Clegg MT (1993) A chloroplast DNA mutational hotspot and gene conversion in a non-coding region near rbcL in the grass family (Poaceae). Curr Genet 24:357-365
18. Ogihara Y, Terachi T, Sasakuma T (1988) Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc Natl Acad Sci USA 85:8573-8577
19. Palmer JD (1991) Plastid chromosomes: structure and evolution. In: Bogorad L, Vasil IK (eds) Cell culture and somatic cell genetics of plants, vol 7A. Academic Press, San Diego, pp 5-53
20. Palmer JD, Jorgensen RA, Thompson WF (1985) Chloroplast DNA variation and evolution in Pisum: patterns of change and phylogenetic analysis. Genetics 109:195-213
21. Palmer JD, Nugent JM, Herbon LA (1987) Unusual structure of geranium chloroplast DNA: a triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families. Proc Natl Acad Sci USA 84:769-773
22. Posno M, van Vliet A, Groot GSP (1986) The gene for Spirodela oligorhiza chloroplasl ribosomal protein homologous to E. coli ribosomal protein L16 is split by a large intron near its 5′ end: structure and expression. Nucleic Acids Res 14:3181-3195
23. Rychlik W, Rhoads RE (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res 17:8543-8551
24. Sugiura M (1989) Oryza sativa chloroplast DNA 134 525 bp. Nagoya University Center for Gene Research, Nagoya, Japan
25. Takaiwa F, Sugiura M (1982) Nucleotide sequence of the 16s-23s spacer region in a rRNA gene cluster from tobacco chloroplast DNA. Nucleic Acids Res 10:2665-2676
26. vanHam RCHJ, t'Hart H, Mes THM, Sandbrink JM (1994) Molecular evolution of non-coding regions of the chloroplast genome in the Crassulaceae and related species. Curr Genet 25:558-566
27. Zurawski G, Clegg MT, Brown AHD (1984) The nature of nucleotide sequence divergence between barley and maize chloroplast DNA. Genetics 106:735-749