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Data base for PCR primers
References

primer papers


Bryan GJ, McNicoll J, Ramsay G, Meyer RC, De Jong WS: Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants. Theoretical and Applied Genetics 1999, 99:859-867.

Campagna ML, Downie SR: 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, 91:1-11.

Demesure B, Sodzi N, Petit RJ: A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 1995, 4:129-131.

Doyle JJ, Davis JI, Soreng RJ, Garvin D, Anderson MJ: Chloroplast DNA Inversions and the Origin of the Glass Family (Poaceae). PNAS 1992, 89:7722-7726.

Doyle JJ, Doyle JL, Palmer JD: Multiple independent losses of two genes and one intron from legume chloroplast genomes. Systematic Botany 1995, 20:272-294.

Dumolin-Lapegue S, Pemonge M-H, Petit RJ: An enlarged set of consensus primers for the study of organelle DNA in plants. Molecular Ecology 1997, 6:393-398.

Fofana B, Harvengt L, Baudoin JP, Dujardin P: New primers for the polymerase chain amplification of cpDNA intergenic spacers in Phaseolus phylogeny. Belgian Journal of Botany 1997, 129:118-122.

Graham SW, Olmstead RG: Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. American Journal of Botany 2000,  87:1712–1730.

Grivet D, Heinze B, Vendramin GG, Petit RJ: Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Molecular Ecology Notes 2001, 1:345-349.

Hamilton MB: Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology 1999, 8:521-523.

Heinze B: PCR-based chloroplast DNA assays for the identification of native Populus nigra and introduced poplar hybrids in Europe. Forest Genetics 1998, 5:31-38.

Hilu KW, Liang H: The matK gene: sequence variation and application in plant systematics. American Journal of Botany 1997, 84:830-839.

Hoot SB, Culham A, Crane PR: 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. 1995, 82:194–207.

Katayama H, Ogihara Y:  Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA. Current Genetics 1996, 29:572-581.

Lee B-Y, Downie SR: Phylogenetic analysis of cpDNA restriction sites and rps16 intron sequences reveals relationships among Apiaceae tribes Caucalideae, Scandiceae, and related taxa. Plant Systematics and Evolution 2000,  221:35-60.

Lee J, Hymowitz T: A Molecular phylogenetic study of the subtribe Glycininae (Leguminosae) derived from the chloroplast DNA rps16 intron sequences. American Journal of Botany 2001, 88:2064–2073.

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.  American Journal of Botany 1992, 79:953-961.

Nakamura I, Kameya N, Kato Y, Yamanaka S, Jomori H, Sato Y: A proposal for identifying the short ID sequence which addresses the plastid subtype of higher plants. Breeding-Science 1997, 47:385-388, 394.

Reeves G, Chase MW, Goldblatt P, Rudall P, Fay MF, Cox AV, Lejeune B, Souza-Chies T: Molecular systematics of Iridaceae: evidence from four plastid DNA regions. American Journal of Botany 2001, 88:2074-2087.

Rieseberg LH, Hanson MA, Philbrick CT: Androdioecy is derived from dioecy in Datiscaceae: evidence from restriction site mapping of PCR-amplified chloroplast DNA fragments. Systematic Botany 1992, 17:324-336.

Rydin C, Källersjö M, Friis EM: 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. 2002, 163:197-214.

Samuel R, Pinsker W, Kiehn M: Phylogeny of some species of Cyrtandra (Cesneriaceae) inferred from the atpB/rbcL cpDNA intergene region. Botanica Acta 1997, 110:503-510.

Savolainen V, Corbaz R, Spichiger R, Manen JF: Chloroplast DNA variation and parentage analysis in 55 apples. Theoretical and Applied Genetics 1995, 90:1138-1141.

Schaffner C, Laasch H, 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. Molecular and General Genetics 1995, 249:533-544.

Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL: The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 2005, 92:142-166.

Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF: The tortoise and the hare: Choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 1998, 85:1301-1315.

Souza-Chies TT, Bittar G, Nadot S, Carter L, Besin E, Lejeune B: Phylogenetic analysis of Iridaceae with parsimony and distance methods using the plastid gene rps4. Plant Systematics and Evolution 1997, 204:109-123.

Taberlet P, Gielly L, Pautou G, Bouvet J: Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 1991, 17:1105-1109.

Tsumura Y, Kawahara T, Wickneswari R, Yoshimura K: Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes. Theoretical and Applied Genetics 1996, 93:22-29.

Tsumura Y, Yoshimura K, Tomaru N, Ohba K: Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theoretical and Applied Genetics 1995, 91:1222-1236.

Weising K, Gardner R: A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 1999, 42:9-19.

Wolfe AD, Elisens WJ, Watson LE, DePamphilis CW: Using restriction-site variation of PCR-amplified cpDNA genes for phylogenetic analysis of three Cheloneae (Scrophulariaceae). American Journal of Botany 1997, 84:555-564.

Ziegenhagen B, Schauerte M, Kormuták A, Scholz F: Plastid DNA polymorphism of megagametophyte and pollen in two Abies species. Silvae Genetica 1996, 45:355-358.

Zurawski G, Clegg MT: Evolution of higher plant chloroplast DNA-encoded genes: implications for structure-function and phylogenetic studies.  Annu. Rev. Plant Physiol. Plant Mol. Biol. 1987, 38:391–418.

other papers cited:

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.

Antoniw J: A new method for designing PCR primers specific for groups of sequences and its application to plant viruses. Molecular Biotechnology 1995, 4:111-119.

Grivet D, Heinze B, Vendramin GG, Petit RJ: Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Molecular Ecology Notes 2001, 1:345-349.

Jackson HD, Steane DA, Potts BM, Vaillancourt RE: Chloroplast DNA evidence for reticulate evolution in Eucalyptus (Myrtaceae). Molecular Ecology 1999, 8:739-751.

Krystufek V: Population genetic analysis of Populus nigra in Austria using nuclear and chloroplast DNA markers. Dissertation, University of Vienna, Austria; 2001.

17.02.06 | Heinze, B.
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