The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans

Molecular Biology and Evolution

Volumn 15, Issue 11, 1998, Pages 1430-1446

  Crease, Teresa J ^a   Taylor, Derek J ^b  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

Branchiopoda; Cladocera; Secondary structure; Slippage replication; SSU rRNA; Variable regions

Indexed keywords

RIBOSOME RNA;

ARTICLE; CRUSTACEA; EVOLUTION; GENETIC VARIABILITY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA GENE; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE HOMOLOGY; ANIMAL; ANOSTRACA; ARTEMIA; CHEMISTRY; COMPARATIVE STUDY; CONFORMATION; DAPHNIA; DNA BASE COMPOSITION; GC RICH SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

ANOMOPODA; ANOSTRACA; ARTEMIA; BRANCHIOPODA; CLADOCERA; CRUSTACEA; CTENOPODA; CYCLESTHERIA; CYCLESTHERIIDAE; CYZICIDAE; DAPHNIA; HAPLOPODA; LAEVICAUDATA; LIMNADIIDAE; NOTOSTRACA; ONYCHOPODA; SPINICAUDATA; TRIOPS;

ANIMALS; ANOSTRACA; ARTEMIA; BASE COMPOSITION; BASE SEQUENCE; CRUSTACEA; DAPHNIA; EVOLUTION, MOLECULAR; GC RICH SEQUENCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 0031787983     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025871     Document Type: Article

References (39)

1. BEATON, M. J. 1988. Genome size variation in the Cladocera. M.Sc. thesis, University of Windsor, Ontario, Canada.
2. _. 1995. Patterns of endopolyploidy and genome size variation in Daphnia. Ph.D. dissertation, University of Guelph, Ontario, Canada.
3. CAMPBELL, B. C., J. D. STEFFEN-CAMPBELL, and R. J. GILL. 1994. Evolutionary origin of whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) inferred from 18S rDNA sequences. Insect Mol. Biol. 3:73-88.
4. CHALWATZIS, N., A. BAUR, E. STETZER, R. KINZELBACH, and F. K. ZIMMERMAN. 1995. Strongly expanded 18S rRNA genes correlated with a peculiar morphology in the insect order Strepsiptera. Zoology 98:115-126.
5. CREASE, T. J., and J. K. COLBOURNE. 1998. The unusually long small-subunit ribosomal RNA of the Crustacean, Daphnia pulex: sequence and predicted secondary structure. J. Mol. Evol 46:307-313.
6. DOYLE, J. J., and J. L. DOYLE. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:11-15.
7. FREIER, S. M., R. KIERZEK, J. A. JAEGER, N. SUGIMOTO, M. H. CARUTHERS, T. NEILSON, and D. H. TURNER. 1986. Improved free-energy parameters for predictions of RNA du-plex stability. Proc. Natl. Acad. Sci. USA 83:9373-9377.
8. FRYER, G. 1987. Morphology and the classification of the socalled Cladocera. Hydrobiologia 145:19-28.
9. GERBI, S. A. 1985. Evolution of ribosomal DNA. Pp. 419-517 in R. J. MACINTYRE, ed. Molecular evolutionary genetics. Plenum Press, New York.
10. GONZALEZ, I. L., J. L. GORSKI, T. J. CAMPEN, D. J. DORNEY, J. M. ERICKSON, J. E. SYLVESTER, and R. D. SCHMICKEL. 1985. Variation among human 28S ribosomal RNA genes. Proc. Natl. Acad. Sci. USA 82:7666-7670.
11. HANCOCK, J. M. 1995. The contribution of DNA slippage to eukaryotic nuclear 18S rRNA evolution. J. Mol. Evol. 40: 629-639.
12. HANCOCK, J. M., and J. S. ARMSTRONG. 1994. SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Comput. Appl. Biosci. 10:67-70.
13. HANCOCK, J. M., and G. A. DOVER. 1988. Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs. Mol. Biol. Evol. 5:377-391.
14. _. 1990. Compensatory slippage in the evolution of ribosomal RNA genes. Nucleic Acids Res. 18:5949-5954.
15. HANCOCK, J. M., D. TAUTZ, and G. A. DOVER. 1988. Evolution of the secondary structures and compensatory mutations of ribosomal RNAs of Drosophila melanogaster. Mol. Biol. Evol. 5:393-414.
16. HASSOUNA, N., B. MICHOT, and J.-P. BACHELLERIE. 1984. The complete nucleotide sequence of mouse 28S rRNA gene: implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Res. 12: 3563-3583.
17. HINKLE, G., D. D. LEIPE, T. A. NERAD, and M. L. SOGIN. 1994. The unusually long small subunit ribosomal DNA of Phreatamoeba balamuthi. Nucleic Acids Res 22:465-469.
18. KUZOFF, R. K., J. A. SWEERE, D. E. SOLTIS, P. S. SOLTIS, and E. A. ZIMMER. 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Mol. Biol. Evol. 15:251-263.
19. KWON, O.-Y., K. OGINO, and H. ISHIKAWA. 1991. The longest 18S ribosomal RNA ever known. Eur. J. Biochem. 202: 827-833.
20. LÉCHER, P., D. DEFAYE, and P. NOEL. 1995. Chromosomal and nuclear DNA of Crustacea. Invertebr. Reprod. Dev. 27:85-114.
21. LEVINSON, G., and G. A. GUTMAN. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:203-221.
22. MATZURA, O., and A. WENNBORG. 1996. RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. CABIOS 12: 247-249.
23. MICHOT, B., and J.-P. BACHELLERIE. 1987. Comparisons of large subunit rRNAs reveal some eukaryote-specific elements of secondary structure. Biochimie 69:11-23.
24. MICHOT, B., L.-H. Qu, and J.-P. BACHELLERIE. 1990. Evolution of large-subunit rRNA structure: the diversification of divergent D3 domain among major phylogenetic groups. Eur. J. Biochem. 188:219-229.
25. NUNN, G. B., B. F. THEISEN, B. CHRISTENSEN, and P. ARCTANDER. 1996. Simplicity-correlated size growth of the nuclear 28S ribosomal RNA D3 expansion segment in the Crustacean order Isopoda. J. Mol. Evol. 42:211-223.
26. OLESON, J., J. W. MARTIN, and E. W. ROESSLER. 1996. External morphology of the male of Cyclestheria hislopi (Baird, 1859)(Crustacea, Branchiopoda, Spinicaudata), with a comparison of male claspers among the Conchostraca and Cladocera and its bearing on phylogeny of the 'bivalved' Branchiopoda. Zool. Scr. 25:291-316.
27. PIÇON, M., R. R. GUTELL, R. EHRLICH, and A. ZAHA. 1996. Characterization of a flatworm ribosomal RNA-encoding gene: promoter sequence and small subunit rRNA secondary structure. Gene 171:215-220.
28. ROESSLER, E. W. 1995. Review of Colombian Conchostraca (Crustacea) - ecological aspects and life cycles - family Cyclestheriidae. Hydrobiologia 298:113-124.
29. ROUSSET, F., M. PELANKADIS, and M. SOLIGNAC. 1991. Evolution of compensatory substitutions through G-U intermediate state in Drosophila rRNA. Proc. Natl. Acad. Sci. USA 88:10032-10036.
30. SANTALUCIA, J., R. KIERZEK, and D. H. TURNER. 1991. Stabilities of consecutive A-C, C-C, C-G, U-C, and U-U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U-U and C-C+ pairs. Biochemistry 30:8242-8251.
31. STAROBOGATOV, Y. I. 1986. Systema rakoobrazayh. Zool. J. 65:1769-1781.
32. SUGIMOTO, N., R. KIERZEK, S. M. FREIER, and D. H. TURNER. 1986. Energetics of internal G-U mismatches in ribooligonucleotide helices. Biochemistry 25:5755-5759.
33. VAN DE PEER, Y., J. JANSEN, P. DERJJK, and R. DE WACHTER. 1997. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 25:111-116.
34. VAWTER, L., and W. M. BROWN. 1993. Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134:597-608.
35. VOGLER, A. P., A. SELSH, and J. M. HANCOCK. 1997. Phylogenetic analysis of slippage-like sequence variation in the V4 rRNA expansion segment in tiger beetles (Cicindelidae). Mol. Biol. Evol. 14:6-19.
36. WALOSSEK, D. 1993. The Upper Cambrian Rehbachiella and the phylogeny of Branchiopoda and Crustacea. Fossils Strata 32:1-202.
37. WILCOX, L. W., L. A. LOUISE, R A. FUERST, and G. L. FLOYD. 1992. Group I introns within the nuclear-encoded small subunit rRNA gene of three green algae. Mol. Biol. Evol. 9: 1103-1118.
38. WINNEPENNINCKX, B., Y. VAN DE PEER, T. BACKEUAU, and R. DE WACHTER. 1995. CARD: a drawing tool for RNA secondary structure models. Biotechniques 18:1060-1063.
39. Wu, M., J. A. McDOWELL, and D. H. TURNER. 1995. A periodic table of symmetric tandem mismatches in RNA. Biochemistry 34:3204-3211.