Mitochondrial sequence evolution in spiders: Intraspecific variation in tRNAs lacking the TΨC arm

Molecular Biology and Evolution

Volumn 17, Issue 7, 2000, Pages 1091-1100

  Masta, Susan E ^a  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

Author keywords

Arthropod systematics; Gene arrangement; Habronattus; Large subunit rRNA structure; Mitochondrial genes; tRNA secondary structure

Indexed keywords

MITOCHONDRIAL RNA;

ARTICLE; DROSOPHILA; MITOCHONDRION; MOLECULAR EVOLUTION; NONHUMAN; RNA SEQUENCE; SPECIES DIFFERENCE; SPIDER;

ARACHNIDA; ARANEAE; ARTHROPODA; CHELICERATA; CRUSTACEA; DROSOPHILA YAKUBA; HABRONATTUS; HEXAPODA; INVERTEBRATA;

EID: 0033945896     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026390     Document Type: Article

References (53)

1. ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHAFFER, J. ZHANG, Z. ZHANG, W. MILLER, and D. J. LIPMAN. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. BARRELL, B. J., S. ANDERSON, A. T. BANKIER et al. (15 coauthors). 1980. Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc. Natl. Acad. Sci. USA 77:3164-3166.
3. BIBB, M. J., R. A. VAN ETTEN, C. T. WRIGHT, M. W. WALBERG, and D. A. CLAYTON. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167-180.
4. BLACK, W. C. IV, and J. PIESMAN. 1994. Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences. Proc. Natl. Acad. Sci. USA 91: 10034-10038.
5. BLACK, W. C. IV, and R. L. ROEHRDANZ. 1998. Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol. Biol. Evol. 15:1772-1785.
6. BOORE, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767-1780.
7. BOORE, J. L., T. M. COLLINS, D. STANTON, L. L. DAEHLER, and W. M. BROWN. 1995. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 376:163-167.
8. BOORE, J. L., D. V. LAVROV, and W. M. BROWN. 1998. Gene translocation links insects and crustaceans. Nature 392:667-668.
9. BÖRNER, G. V., S. YOKOBORI, M. MÖRL, M. DÖRNER, and S. PÄÄBO. 1997. RNA editing in metazoan mitochondria: staying fit without sex. FEBS Lett. 409:320-324.
10. CAMPBELL, N. J. H., and S. C. BARKER. 1998. An unprecedented major rearrangement in an arthropod mitochondrial genome. Mol. Biol. Evol. 15:1786-1787.
11. _. 1999. The novel mitochondrial gene arrangement of the cattle tick, Boophilus microplus: fivefold tandem repetition of a coding region. Mol. Biol. Evol. 16:732-740.
12. CLARY, D. O., and D. R., WOLSTENHOLME. 1985. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J. Mol. Evol. 22:252-271.
13. CROOM, H. B., R. G. GILLESPIE, and S. R. PALUMBI. 1991. Mitochondrial DNA sequences coding for a portion of the RNA small ribosomal subunits of Tetragnatha madibulata and Tetragnatha hawaiensis (Araneae, Tetragnathidae). J. Arachnol. 19:210-214.
14. DE BRUIJN, M. H. L. 1983. Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code. Nature 304:234-241.
15. DIRHEIMER, G., G. KEITH, P. DUMAS, and E. WESTHOF. 1995. Primary, secondary, and tertiary structures of tRNAs. Pp. 93-126 in D. SÖLL and L. RAJBHANDARY, eds. tRNA: structure, biosynthesis, and function. ASM Press, Washington, D.C.
16. FRATI, F., C. SIMON, J. SULLIVAN, and D. L. SWOFFORD. 1997. Evolution of the mitochondrial cytochrome oxidase gene II in Collembola. J. Mol. Evol. 44:145-158.
17. GILBERT, D. 1994. SeqApp: a biosequence editor and analysis application. Distributed by the author, Indiana University.
18. GUTELL, R. R. 1993. Comparative studies of RNA: inferring higher-order structure from patterns of sequence variation. Curr. Opin. Struct. Biol. 3:313-322.
19. _. 1994. Secondary structure of the mitochondrial large ribosomal subunit of Caenorhabditis elegans. http./pundit. icmb.utexas.edu/RNA/23S.
20. _. 1996. Comparative sequence analysis and the structure of 16S and 23S rRNA. Pp. 111-128 in R. A. ZIMMERMAN and A. E. DAHLBERG, eds. Ribosomal RNA. Structure, evolution, processing, and function in protein biosynthesis. CRC Press, New York.
21. GUTELL, R. R., and G. E. Fox. 1988. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 16:r175-r313.
22. HAUCKE, H.-R., and G. GELLISSEN. 1988. Different mitochondrial gene orders among insects: exchanged tRNA gene positions in the COII/COIII region between an orthopteran and a dipteran species. Curr. Genet. 14:471-476.
23. HEDIN, M. C. 1997a. Molecular phylogenetics at the populations/species interface in cave spiders of the southern Appalachians (Araneae: Nesticidae: Nesticus). Mol. Biol. Evol. 14:309-324.
24. _. 1991 b. Speciational history in a diverse clade of habitat-specialized spiders (Araneae: Nesticidae: Nesticus): inferences from geographic-based sampling. Evolution 51: 1929-1945.
25. HUBER, K. C., T. S. HAIDER, M. W. MÜLLER, B. A. HUBER, R. J. SCHWEYEN, and F. G. BARTH. 1993. DNA sequence data indicates the polyphyly of the family Ctenidae (Araneae). J. Arachnol. 21:194-201.
26. KEDDIE, E. M., T. HIGAZI, and T. R. UNNASCH. 1998. The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis. Mol. Biochem. Parasitol. 95:111-127.
27. KUMAZAWA, Y., and M. NISHIDA. 1993. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37:380-398.
28. KUMAZAWA, Y., H. OTA, M. NISHIDA, and T. OZAWA. 1996. Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Mol. Biol. Evol. 13:1242-1254.
29. LONERGAN, K. M., and M. W. GRAY. 1993. Editing of transfer RNAs in Acanthamoeba castellanii mitochondria. Science 259:812-816.
30. LIU, H., and A. T. BECKENBACH. 1992. Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects. Mol. Phylogenet. Evol. 1:41-52.
31. LYNCH, M. 1996. Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 13:209-220.
32. MACEY, J. R., A. LARSON, N. B. ANANJEVA, and T. J. PAPENFUSS. 1997. Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs. Mol. Biol. Evol. 14:30-39.
33. MADDISON, W. P., and D. R. MADDISON. 1992. MacClade: analysis of phylogeny and character evolution. Version 3.0. Sinauer, Sunderland, Mass.
34. MINDELL, D. P., M. D. SORENSON, and D. E. DIMCHEFF. 1998. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. USA 95:10693-10697.
35. NEDELCU, A. M. 1997. Fragmented and scrambled mitochondrial ribosomal RNA coding regions among green algae: a model for their origin and evolution. Mol. Biol. Evol. 14: 506-517.
36. OKIMOTO, R., J. L. MACFARLANE, D. O. CLARY, and D. R. WOLSTENHOLME. 1992. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130:471-498.
37. OKIMOTO, R., J. L. MACFARLANE, and D. R. WOLSTENHOLME. 1990. Evidence for the frequent use of TTG as the translation initiation codon of mitochondrial protein genes in the nematodes, Ascaris suum and Caenorhabditis elegans. Nucleic Acids Res. 18:6113-6118.
38. OKIMOTO, R., and D. R. WOLSTENHOLME. 1990. A set of tRNAs that lack either the TΨPC arm or the dihydrouridine arm: towards a minimal tRNA adaptor. EMBO J. 9:3405-3411.
39. SIMON, C., F. FRATI, A. BECKENBACH, B. CRESPI, H. LIU, and P. FLOOK. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain-reaction primers. Ann. Entomol. Soc. Am. 87:651-701.
40. SMITH, M. F., W. K. THOMAS, and J. L. PATTON. 1992. Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent. Mol. Biol. Evol. 9:204-215.
41. STATON, J. L., L. L. DAEHLER, and W. M. BROWN. 1997. Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L: conservation of major features among arthropod classes. Mol. Biol. Evol. 14:867-874.
42. SUNNUCKS, P., and D. F. HALES. 1996. Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Mol. Biol. Evol. 13:510-524.
43. SWOFFORD, D. L. 1998. PAUP*4.0: Phylogenetic analysis using parsimony. Sinauer, Sunderland, Mass.
44. TATUSOVA, T. A., and T. L. MADDEN. 1999. BLAST 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174:247-250.
45. TERRETT, J. A., S. MILES, and R. H. THOMAS. 1996. Complete DNA sequence of the mitochondrial genome of Cepaea nemoralis (Gastropoda: Pulmonata). J. Mol. Evol. 42:160-168.
46. VALVERDE, J., R. MARCO, and R. GARESSE. 1994. A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria. Proc. Natl. Acad. Sci. USA 91:5368-5371.
47. WATANABE, Y.-I., H. TSURUI, T. UEDA, R. FURUSHIMA, S. TAKAMIYA, K. KITA, K. NISHIKAWA, and K. WATANABE. 1994. Primary and higher order structures of nematode (Ascaris suum) mitochondrial tRNAs lacking either the T or D stem. J. Biol. Chem. 269:22902-22906.
48. WOLSTENHOLME, D. R. 1992. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141:173-216.
49. WOLSTENHOLME, D. R., J. L. MACFARLANE, R. OKIMOTO, D. O. CLARY, and J. A. WAHLEITHNER. 1987. Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proc. Natl. Acad. Sci. USA 84:1324-1328.
50. YAMAZAKI, N., R. UESHIMA, J. A. TERRETT et al. (12 co-authors). 1997. Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics 145:749-758.
51. YOKOBORI, S., and S. PÄÄBO. 1995a. tRNA editing in metazoans. Nature 377:490.
52. _. 1995b. Transfer RNA editing in land snail mitochondria. Proc. Natl. Acad. Sci. USA 92:10432-10435.
53. ZHANG, D.-X., and G. M. HEWITT. 1996. Nuclear integrations: challenges for mitochondrial DNA markers. Trends Ecol. Evol. 11:247-251.