A data base for PCR primers in the chloroplast genome
References

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Introduction
Methods
The data base, and some applications
Conclusions
References
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References

Primer papers:

Bryan, G. J. and J. McNicoll, G. Ramsay R. C. Meyer W. S. De Jong. Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants. Theoretical and Applied Genetics 99(5), 859-867. 1999.
Campagna, M. L., Stephen R. Downie. The Intron in Chloroplast Gene rpl16 is Missing From the Flowering Plant Families Geraniaceae, Goodeniaceae, and Plumbaginaceae. Transactions of the Illinois State Academy of Science (1998), Volume 91, 1 and 2, pp.1-11
Demesure, B., Sodzi, N., and Petit, R. J. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol. Ecol. 4, 129-131. 1995.
Doyle, J. J. and JI Davis, RJ Soreng D Garvin and MJ Anderson. Chloroplast DNA Inversions and the Origin of the Glass Family (Poaceae). PNAS 89: 7722 - 7726 . 1992.
Doyle, J. J., Doyle, J. L., and Palmer, J. D. Multiple independent losses of two genes and one intron from legume chloroplast genomes. Systematic Botany 20, 272-294. 1995.
Dumolin-Lapegue, S., Pemonge, M.-H., and Petit, R. J. An enlarged set of consensus primers for the study of organelle DNA in plants. Mol. Ecol. 6, 393-398. 1997.
Fofana, B., Harvengt, L., Baudoin, J. P., and Dujardin, P. New primers for the polymerase chain amplification of cpDNA intergenic spacers in Phaseolus phylogeny. Belgian Journal of Botany 129, 118-122. 1997.
Graham, S. W. and Olmstead, R. G. Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. American Journal of Botany 87(11), 1712–1730. 2000.
Grivet, D., Heinze, B., Vendramin, G. G., and Petit, R. J. Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Molecular Ecology Notes 1(4), 345-349. 2001.
Hamilton, M. B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 8, 521-523. 1999.
Heinze, B. PCR-based chloroplast DNA assays for the identification of native Populus nigra and introduced poplar hybrids in Europe. Forest Genetics 5(1), 31-38. 1998.
Hilu, K. W. and Liang, H. The matK gene: sequence variation and application in plant systematics. Am. J. Bot. 84, 830-839. 1997.
Hoot, S. B., Culham, A., and Crane, P. R. The utility of atpB gene sequences in resolving phylogenetic relationships: comparison with rbcL and 18S ribosomal DNA sequences in the Lardizabalaceae. Ann Mo Bot Gard 82:194–207. 1995.
Katayama, H. and Ogihara, Y. Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA. Current Genetics Volume 29, Issue 6, pp 572-581. 1996.
Lee, B.-Y. and S. R. Downie. Phylogenetic analysis of cpDNA restriction sites and rps16 intron sequences reveals relationships among Apiaceae tribes Caucalideae, Scandiceae, and related taxa. Plant Systematics and Evolution 221: 35-60. 2000.
Lee, K. and Theodore Hymowitz. A Molecular Phylogenetic Study Of The Subtribe Glycininae (Leguminosae) Derived From The Chloroplast DNA rps16 Intron Sequences. American Journal of Botany 88(11): 2064-2073. 2001.
Liston, A. Variation in the chloroplast genes rpoC1 and rpoC2 of the genus Astralagus (Fabaceae): evidence from restriction site mapping of a PCR-amplified fragment. Am. J. Bot. 79, 953-961. 1992.
Nakamura I, Kameya N, Kato Y, Yamanaka S, Jomori H, and Sato Y. A proposal for identifying the short ID sequence which addresses the plastid subtype of higher plants. Breeding-Science. 1997, 47: 4, 385-388, 394; 19 ref. 1997.
Reeves, G., Mark W. Chase, Peter Goldblatt, Paula Rudall, Michael F. Fay, Anthony V. Cox, Bernard Lejeune and Tatiana Souza-Chies. Molecular systematics of Iridaceae: evidence from four plastid DNA regions. American Journal of Botany 88(11): 2074-2087. 2001
Rieseberg, L. H., Hanson, M. A., and Philbrick, C. T. Androdioecy is derived from dioecy in Datiscaceae: evidence from restriction site mapping of PCR-amplified chloroplast DNA fragments. Systematic Botany 17, 324-336. 1992.
Rydin, C., Källersjö, M., and Friis, E. M. Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: conflicting data, rooting problems, and the monophyly of conifers. Int. J. Plant Sci. 163(2):197-214. 2002.
Samuel, R., Pinsker, W., and Kiehn, M. Phylogeny of some species of Cyrtandra (Cesneriaceae) inferred from the atpB/rbcL cpDNA intergene region. Botanica Acta 110, 503-510. 1997.
Savolainen, V., Corbaz, R., Spichiger, R., and Manen, J. F. Chloroplast DNA variation and parentage analysis in 55 apples. Theoretical and Applied Genetics 90, 1138-1141. 1995.
Souza-Chies, T. T., Bittar, G., Nadot, S., Carter, L., Besin, E., and Lejeune, B. Phylogenetic analysis of Iridaceae with parsimony and distance methods using the plastid gene rps4. Plant Systematics and Evolution 204, 109-123. 1997.
Schaffner, C, Laasch, H, and Hagemann, R. Detection of point mutations in chloroplast genes of Antirrhinum majus L. I. Identification of a point mutation in the psaB gene of a photosystem I plastome mutant. Mol Gen Genet 249, 533-544. 1995.
Taberlet, P., Gielly, L., Pautou, G., and Bouvet, J. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17, 1105-1109. 1991.
Tsumura, Y., Yoshimura, K., Tomaru, N., and Ohba, K. Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theoretical and Applied Genetics 91, 1222-1236. 1995.
Tsumura, Y., Kawahara, T., Wickneswari, R., and Yoshimura, K. Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes. Theoretical and Applied Genetics 93, 22-29. 1996.
Weising, K. and Gardner, R. A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 42, 9-19. 1999.
Wolfe, A. D., Elisens, W. J., Watson, L. E., and DePamphilis, C. W. Using restriction-site variation of PCR-amplified cpDNA genes for phylogenetic analysis of three Cheloneae (Scrophulariaceae). Am J Bot 84(4), 555-564. 1997.
Ziegenhagen, B., Schauerte, M., Kormuták, A., and Scholz, F. Plastid DNA polymorphism of megagametophyte and pollen in two Abies species. Silvae Genetica 45, 355-358. 1996.
Zurawski, G. and Clegg, M. T. Evolution of higher plant chloroplast DNA-encoded genes: implications for structure-function and phylogenetic studies. Annu Rev Plant Physiol Plant Mol Biol 38: 391–418. 1987.

other papers cited:

Altschul, S. F. and Thomas L. Madden, Alejandro A. Schäffer Jinghui Zhang Zheng Zhang Webb Miller and David J. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. 1997
Antoniw, J. A new method for designing PCR primers specific for groups of sequences and its application to plant viruses. Molecular Biotechnology 4, 111-119. 1995.
Grivet, D., Heinze, B., Vendramin, G. G., and Petit, R. J. Shifts in chloroplast genome size across angiosperm lineages. Plant and Animal Genome VIII, January 2000, San Diego, CA (Poster) . 2000.
Krystufek, V.: Population genetic analysis of Populus nigra in Austria using nuclear and chloroplast DNA markers. Dissertation, University of Vienna, Austria, 2001.
Jackson, H. D. and D. A. Steane, B. M. Potts & R. E. Vaillancourt. Chloroplast DNA evidence for reticulate evolution in Eucalyptus (Myrtaceae). Mol. Ecol. 8(5), 739-751. 1999.

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