Secondary Structure and Molecular Evolution of the Mitochondrial Small Subunit Ribosomal RNA in Agaricales (Euagarics clade, Homobasidiomycota)

Journal of Molecular Evolution

Volumn 57, Issue 4, 2003, Pages 383-396

  Barroso, Gérard ^a   Sirand Pugnet, Pascal ^a   Mouhamadou, Bello ^a   Labarère, Jacques ^a  

^a UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

Hairpin; Homobasidiomycota; Insertion deletion; Mitochondria; Mushroom; SSU rRNA; Variable domains

Indexed keywords

PRIMER DNA; RECOMBINANT RNA; SMALL SUBUNIT RIBOSOMAL RNA;

AGARICALES; AGARICUS BISPORUS; AMINO ACID SUBSTITUTION; ARCHAEBACTERIUM; ARTICLE; EXPERIMENTAL MODEL; GENE CLUSTER; GENE DELETION; GENE INSERTION; GENE SEQUENCE; LENTINUS EDODES; MITOCHONDRION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MUSHROOM; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASTID; PROTEIN DOMAIN; RNA STRUCTURE; SIGNAL TRANSDUCTION; STREPTOCOCCACEAE; STREPTOCOCCUS COMMUNE; STRUCTURE ANALYSIS;

AGARICALES; BASE SEQUENCE; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GENE DELETION; LENTINULA; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; NUCLEIC ACID CONFORMATION; RNA; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

AGARICALES; AGARICUS; AGARICUS BISPORUS; AGROCYBE AEGERITA; ARCHAEA; BASIDIOMYCOTA; INSERTION SEQUENCES; LENTINULA; LENTINULA EDODES; LENTINUS; SCHIZOPHYLLUM; SCHIZOPHYLLUM COMMUNE; STREPTOCOCCACEAE; STREPTOCOCCUS;

EID: 0142012119     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2487-5     Document Type: Article

References (30)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Barroso G, Blesa S, Labarère J (1995) Wide distribution of mitochondrial genome rearrangements in wild strains of the basidiomycete Agrocybe aegerita. Appl Environ Microbiol 61:1187-1193
3. Barroso G, Blesa S, Labarère J (1995) Wide distribution of mitochondrial genome rearrangements in wild strains of the basidiomycete Agrocybe aegerita. Appl Environ Microbiol 61:1187-1193
4. Bruns TD, Szaro TM, Gardes M, Cullings KW, Pan JJ, Taylor DL, et al. (1998) A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis. Molecular Ecology 7:257-272
5. Bruns TD, Szaro TM (1992) Rate and mode differences between nuclear and mitochondrial small-subunit rRNA genes in Mushrooms. Mol Biol Evol 9:836-855
6. Choe CP, Hwang UW, Kim W (1999) Putative secondary structures of unusually long strepsipteran SSU-rRNAs and its phylogenetic implications. Mol Cells 9:191-199
7. Fukumasa-nakai Y, Matsumoto T, Fukuda M (1992) Efficient isolation of mitochondrial DNA from higher Basidiomycetes for restriction endonuclease analysis. Rept Tottori Mycol Inst 30:60-68
8. Gonzalez P, Barroso G, Labarère J (1997) DNA sequence and secondary structure of the mitochondrial small subunit ribosomal RNA coding region including a group-IC2 intron from the cultivated basidiomycete Agrocybe aegerita. Gene 184:55-63
9. Gonzalez P, Barroso G, Labarère J (1999) Molecular gene organisation and secondary structure of the mitochondrial large subunit ribosomal RNA from the cultivated Basidiomycota Agrocybe aegerita: A 13 kb gene possessing six unusual nucleotide extensions and eight introns. Nuc Acids Res 27:1754-1761
10. Gonzalez P, Labarère J (1999) Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6, and V9 domains reveal highly species-specific variations within the genus Agrocybe. Appl Environ Microbiol 64:4149-4160
11. Gonzalez P, Labarère J (2000) Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial SSU-rRNA V4, V6 and V9 domains. Microbiology 146:209-221
12. Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Science 283:1476-1481
13. Hibbett DS, Donoghue MJ (1994) Progress toward a phylogenetic classification of the polyporaceae through parsimony analysis of mitochondrial ribosomal DNA sequences. Can J Bot 73:S853-S861
14. Hibbett DS, Pine EM, Langer E, Langer G, Donoghue MJ (1997) Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc Natl Acad Sci USA 94:1202-1206
15. Higgins DG, Sharp PM (1989) Fast and sensitive multiple alignment sequence on a microcomputer. Comput Appl Biosci 5:151-153
16. Maniatis T, Frisch EF, Hoffman J (1982) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
17. Michel F, Westhof E (1990) Modeling of the three-dimensional architecture of group-I catalytic introns based on comparative sequence analysis. J Mol Biol 216:586-610
18. Moncalvo JM, Drehmel D, Vilgalys R (2000) Variations in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushrooms genus Amanita (Agaricales, Basidiomycota): Phylogenetic implications. Mol Phylogenet Evol 16:48-63
19. Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R (1993) Complilation of small ribosomal subunit RNA structures. Nuc Acids Res 21:3025-3049
20. Noël T, Labarère J (1987) Isolation of DNA from Agrocybe aegerita for the construction of a genomic library in Escherichia coli. Mushroom Science 12:187-201
21. Okamoto K, Sekito T, Yoshida K (1996) The secondary structure and phylogenetic relationship deduced from complete nucleotide sequence of mitochondrial small subunit rRNA in yeast Hansenula wingei. Genes Genet Syst 71(2):69-74
22. Page RDM (2000) Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching. Nuc Acids Res 28:3839-3845
23. Raper JR, Hoffman RM (1974) Schizophyllum commune. In: RC King (ed) Handbook of genetics, volume 1. Plenum Press, New York, pp 597-626
24. Sanger F, Nicklen S, Coulson AR (1977) Sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467
25. Southern E (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Biol Chem 98:503-517
26. Winberly BT, Brodersen DE, Demons WM, Morgan-Warren RJ, Carter AP, Vonrheim C, et al. (2000) Structure of the 30S ribosomal subunit. Nature 407:327-339
27. Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R (2002) The European database on small subunit ribosomal RNA. Nucl Acids Res 30:183-185
28. Wuyts J, Van de Peer Y, De Wachter R (2001) Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucl Acids Res 29:5017-5028
29. Yanisch-Perron C, Viera J, Messing J (1985) Improved M13 cloning vectors and host strains: nucleotide sequences of the M13 mp18 and pUC19 vectors. Gene 33:103-119
30. Zuker M, Jacobson AB (1995) "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA. Nucl Acids Res 23:2791-2798