The complete plastid genome sequence of Angiopteris evecta (G. Forst.) Hoffm. (Marattiaceae)

American Fern Journal

Volumn 97, Issue 2, 2007, Pages 95-106

  Roper, Jessie M ^a   Hansen, S Kellon ^a   Wolf, Paul G ^a   Karol, Kenneth G ^b   Mandoli, Dlna F ^b   Everett, Karin D E ^b   Kuehl, Jennifer ^c   Boore, Jeffrey L ^c  

^a UTAH STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADIANTUM; ANGIOPTERIS; ANGIOPTERIS EVECTA; FILICOPHYTA; MARATTIACEAE; PSILOTUM; VIRIDIPLANTAE;

EID: 34548268037     PISSN: 00028444     EISSN: None     Source Type: Journal    
DOI: 10.1640/0002-8444(2007)97[95:TCPGSO]2.0.CO;2     Document Type: Article

References (39)

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. Nucl. Acids Res. 25:3389-3402.
2. COSNER, M. A., L. A. RAUBESON and R. K. JANSEN. 2004. Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evol. Biol. 4:1-17.
3. DEAN, F. B., J. R. NELSON, T. L. GIESLER and R. S. LASKEN. 2001. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle. Genome Res. 11:1095-1099.
4. ELKIN, C. J., P. M. RICHARDSON, H. M. FOURCADE, N. M. HAMMON, M. J. POLLARD, P. F. PREDKI, T. GLAVINA and T. L. HAWKINS. 2001. High-throughput plasmid purification for capillary sequencing. Genome Res. 11:1269-1274.
5. EWING, B. and P. GREEN. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
6. EWING, B., L. HILLIER, M. C. WENDL and P. GREEN. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
7. FREYER, R., M.-C. KIEFER-MAYER and H. KOSSEL. 1997. Occurrence of plastid RNA editing in all major lineages of land plants. Proc. Natl. Acad. Sci. (USA) 94:6285-6290.
8. GORDON, D., C. ABAIIAN and P. GREEN. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
9. GOULDING, S. E., R. G. OLMSTEAD, C. W. MORDEN and K. H. WOLFE. 1996. Ebb and flow of the chloroplast inverted repeat. Mol. Gen. Genet. 252:195-206.
10. HASEBE, M. and K. IWATSUKI. 1992. Gene localization on the chloroplast DNA of the maiden hair fern: Adiantum capillis-veneris. Bot. Mag. Tokyo 105:413-419.
11. HASEBE, M., T. OMORI, M. NAKAZAWA, T. SANO, M. KATO and K. IWATSUKI. 1994. RbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns. Proc. Natl. Acad. Sci. (USA) 91:5730-5734.
12. HASEBE, M., P. G. WOLF, K. M. PRYER, K. UEDA, M. ITO, R. SANO, G. J. GASTONY, J. YOKOYAMA, J. R. MANHART, N. MURAKAMI, E. H. CRANE, C. H. HAUFLER and W. D. HAUK. 1995. Fern phylogeny based on rbcL nucleotide sequences. Amer. Fern J. 85:134-181.
13. HILL, C. R. and J. M. CAMUS. 1986. Evolutionary cladistics of marattialian ferns. Bull. Brit. Mus. (Nat. Hist.), Botany Series 14:219-300.
14. KENRICK, P. and P. R. CRANE. 1997. The Origin and Early Diversification of Land Plants: A Cladistic Study. Smithsonian Press, Washington, DC, U.S.A.
15. KUGITA, M., Y. YAMAMOTO, T. FUJIKAWA, T. MATSUMOTO and K. YOSHINAGA. 2003. RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucl. Acids Res. 31:2417-2423.
16. KURTZ, S., J. V. CHOUDHURI, E. OHLEBUSCH, C. SCHLEIERMACHER, J. STOYE and R. GIEGERICH. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucl. Acids Res. 29:4633-4642.
17. OLDENBURG, D. J. and A. J. BENDICH. 2004. Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms. J. Mol. Biol. 335:953-970.
18. PALMER, J. D. 1983. Chloroplast DNA exists in two orientations. Nature 301:92-93.
19. PALMER, J. D. 1985. Comparative organization of chloroplast genomes. Ann. Rev. Genet. 19:325-354.
20. PALMER, J. D. 1991. Plastid Chromosomes: Structure and Evolution. Pp. 5-53, in L. Bogorad, ed. Molecular biology of plastids. Academic Press, Orlando, FL.
21. PALMER, J. D., J. M. NUGENT and L. A. HERBON. 1987a. 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. PALMER, J. D., B. OSORIO, J. ALDRICH and W. F. THOMPSON. 1987b. Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr. Genet. 11:275-286.
23. PRYER, K. M., H. SCHNEIDER and S. MAGALLÓ N. 2004a. The radiation of Vascular plants. In J. Cracraft and M. J. Donoghue, eds. Assembling the Tree of Life. Oxford University Press, New York.
24. PRYER, K. M., E. SCHUETTPELZ, P. G. WOLF, H. SCHNEIDER, A. R. SMITH and R. CRANFILL. 2004b. Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences. Amer. J. Bot. 91:1582-1598.
25. PRYER, K. M., H. SCHNEIDER, A. R. SMITH, R. CRANFILL, P. G. WOLF, J. S. HUNT and S. D. SIPES. 2001. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409:618-622.
26. RAUBESON, L. A. and R. K. JANSEN. 1992. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255:1697-2699.
27. RAUBESON, L. A. and D. B. STEIN. 1995. Insights into fern evolution from mapping chloroplast genomes. Amer. Fern J. 85:193-204.
28. SAMBROOK, E., F. FRITCH and T. MANIATIS. 1989. Molecular Cloning: A Laboratory Manual, 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
29. SMALL, R. L., E. B. LICKEY, J. SHAW and W. D. HAUK. 2005. Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae. Mol. Phylogenet. and Evol. 36:509-522.
30. SMITH, A. R., K. M. PRYER, E. SCHUETTPELZ, P. KORALL, H. SCHNEIDER and P. G. WOLF. 2006. A classification of extant ferns. Taxon 55:705-731.
31. SOLTIS, P. S., D. E. SOLTIS, V. SAVOLAINEN, P. R. CRANE and T. G. BARRACLOUGH. 2002. Rate heterogenity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils. Proc. Natl. Acad. Sci. (USA) 99:4430-4435.
32. STEIN, D. B., J. D. PALMER and W. F. THOMPSON. 1986. Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda. Current Genetics 10:835-841.
33. STEIN, D. B., G. YATSKIEVYCH and G. J. GASTONY. 1989. Chloroplast DNA evolution and phylogeny of some polystichoid ferns. Biochem. Syst. Ecol. 17:93-101.
34. STEIN, D. B., D. S. CONANT, M. E. AHEARN, E. T. JORDAN, S. A. KIRCH, M. HASEBE, K. IWATSUKI, M. K. TAN and J. A. THOMASON. 1992. Structural rearrangements of the chloroplast genome provide an important phylogenetic link in ferns. Proc. Natl. Acad. Sci. (USA) 89:1856-1860.
35. STEWART, W. W. and G. W. ROTHWELL. 1993. Paleobotany and the Evolution of Plants. Cambridge University Press, Cambridge.
36. WILKSTRÖM, N. and K. M. PRYER. 2005. Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails. Mol. Phylogenet. and Evol. 36:484-493.
37. WOLF, P. G., C. A. ROWE and M. HASEBE. 2004. High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris. Gene 339:89-97.
38. WOLF, P. G., C. A. ROWE, R. B. SINCLAIR and M. HASEBE. 2003. Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Res. 10:59-65.
39. WYMAN, S. K., J. L. BOORE and R. K. JANSEN. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics.