The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)

Gene

Volumn 350, Issue 2, 2005, Pages 117-128

  Wolf, Paul G ^a   Karol, Kenneth G ^b   Mandoli, Dina F ^b   Kuehl, Jennifer ^c   Arumuganathan, K ^d   Ellis, Mark W ^a   Mishler, Brent D ^e   Kelch, Dean G ^e   Olmstead, Richard G ^b   Boore, Jeffrey L ^c,e  

^a UTAH STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d BENAROYA RESEARCH INSTITUTE   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Evolution; Gene order; Organelle

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CHLOROPLAST GENETICS; COMPARATIVE STUDY; DATA BASE; FLUORESCENCE ACTIVATED CELL SORTING; GENE AMPLIFICATION; GENE ORDER; GENE SEQUENCE; HUPERZIA; LIVERWORT; LYCOPODIACEAE; MOSS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; VASCULAR PLANT;

CHROMOSOME MAPPING; DNA, CHLOROPLAST; GENE ORDER; HUPERZIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

ANTHOCEROTOPHYTA; BRYOPHYTA; BRYOPHYTES; HUPERZIA; HUPERZIA LUCIDULA; LYCOPODIACEAE; LYCOPODIOPHYTA; MARCHANTIOPHYTA; TRACHEOPHYTA; VIRIDIPLANTAE;

EID: 21144458976     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2005.01.018     Document Type: Article

References (36)

1. S.F. Altschul Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
2. T.J. Barkman Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny Proc. Natl. Acad. Sci. U. S. A. 97 2000 13166 13171
3. J.L. Boore Animal mitochondrial genomes Nucleic Acids Res. 27 1999 1767 1780
4. F.B. Dean, J.R. Nelson, T.L. Giesler, and R.S. Lasken Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle Genome Res. 11 2001 1095 1099
5. O. Dombrovska, and Y.L. Qiu Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications Mol. Phylogenet. Evol. 32 2004 246 263
6. C. Elkin Magnetic bead purification of labeled DNA fragments for high-throughput capillary electrophoresis sequencing BioTechniques 32 2002 1296 1302
7. B. Ewing, and P. Green Base-calling of automated sequencer traces using phred: II. Error probabilities Genome Res. 8 1998 186 194
8. J. Felsenstein PHYLIP vs. 3.6. Computer program distributed by Department of Genetics 2004 University of Washington Seattle, WA
9. D. Gordon, C. Abajian, and P. Green Consed: a graphical tool for sequence finishing Genome Res. 8 1998 195 202
10. V.V. Goremykin, K.I. Hirsch-Ernst, S. Wolfl, and F.H. Hellwig The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm Mol. Biol. Evol. 21 2004 1445 1454
11. S.E. Goulding, R.G. Olmstead, C.W. Morden, and K.H. Wolfe Ebb and flow of the chloroplast inverted repeat Mol. Gen. Genet. 252 1996 195 206
12. S.W. Graham, P.A. Reeves, A.C.E. Burns, and R.G. Olmstead Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference Int. J. Plant Sci. 161 2000 S83 S96
13. M. Hasegawa, A. Dirienzo, T.D. Kocher, and A.C. Wilson Toward a more accurate time-scale for the human mitochondrial-DNA tree J. Mol. Evol. 37 1993 347 354
14. K.G. Helfenbein, and J.L. Boore The mitochondrial genome of Phoronis architecta-comparisons demonstrate that phoronids are lophotrochozoan protostomes Mol. Biol. Evol. 21 2004 153 157
15. S.Y.W. Ho, and L.S. Jermiin Tracing the decay of the historical signal in biological sequence data Syst. Biol. 53 2004 623 637
16. D.T. Jones, W.R. Taylor, and J.M. Thornton The rapid generation of mutation data matrices from protein sequences Comput. Appl. Biosci. 8 1992 275 282
17. D.G. Kelch, A. Driskell, and B.D. Mishler Inferring phylogeny using genomic characters: a case study using land plant plastomes B. Goffinet V. Hollowell R. Magill Monographs in systematic botany from the Missouri botanical garden Molecular Systematics of Bryophytes vol. 98 2004 MBG Press St. Louis, MO, USA 3 11
18. P. Kenrick, and P.R. Crane The origin and early diversification of land plants: a cladistic study 1997 Smithsonian Press Washington, DC, USA
19. K.-J. Kim, and H.-L. Lee Complete chloroplast genome sequences from Korean Ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants DNA Res. 11 2004 247 261
20. M. Kugita, Y. Yamamoto, T. Fujikawa, T. Matsumoto, and K. Yoshinaga RNA editing in hornwort chloroplasts makes more than half the genes functional Nucleic Acids Res. 31 2003 2417 2423
21. C. Lemieux, C. Otis, and M. Turmel Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution Nature 403 2000 649 652
22. P.J. Lockhart, M.A. Steel, M.D. Hendy, and D. Penny Recovering evolutionary trees under a more realistic model of sequence evolution Mol. Biol. Evol. 11 1994 605 612
23. W.P. Maddison, and D.R. Maddison MacClade: analysis of phylogeny and character evolution 2003 Sinauer Sunderland, MA Version 4.0b6
24. B.D. Mishler Deep phylogenetic relationships among "plants" and their implications for classification Taxon 49 2000 661 683
25. T. Nishiyama Chloroplast phylogeny indicates that bryophytes are monophyletic Mol. Biol. Evol. 21 2004 1 7
26. D. Normile Evolutionary genomics-the ups and downs of evolution Science 294 2001 2281 2282
27. J.D. Palmer, and D.B. Stein Conservation of chloroplast genome structure among vascular plants Curr. Genet. 10 1986 823 833
28. L.A. Raubeson, and R.K. Jansen Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants Science 255 1992 1697 2699
29. I.A. Shahmuradov, Y.Y. Akbarova, V.V. Solovyev, and J.A. Aliyev Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis Plant Mol. Biol. 52 2003 923 934
30. D.E. Soltis Genome-scale data, angiosperm relationships, and 'ending incongruence': a cautionary tale in phylogenetics Trends Plant Sci. 9 2004 477 483
31. S. Stefanovic, D.W. Rice, and J.D. Palmer Long branch attraction, taxon sampling, and the earliest angiosperm: Amborella or monocots? BMC Evol. Biol. 4 2004 35
32. B. Stoebe, S. Hansmann, V. Goremykin, K.V. Kowalik, and W. Martin Proteins encoded in sequenced chloroplast genomes: an overview of gene content, phylogenetic information and endosymbiotic gene transfer to the nucleus P.M. Hollingsworth R.M. Batesman R.J. Gornall Molecular systematics and plant evolution 1999 Taylor & Francis London 327 352
33. K. Strimmer, and A.v. Haeseler Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies Mol. Biol. Evol. 13 1996 964 969
34. D.L. Swofford PAUP*: phylogenetic analysis using parsimony (* and other methods) version 4 2003 Sinauer Associates Sunderland, MA
35. D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis Phylogenetic inference D.M. Hillis C. Moritz B.K. Mable Molecular systematics Second edition 1996 Sinauer Sunderland, MA 407 514
36. P.G. Wolf, C.A. Rowe, and M. Hasebe High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris Gene 339 2004 89 97