Primer 1 – BLAST unknown - The Parasitic Plant Connection

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Low Copy Nuclear Genes Used in Species-Level Studies of Plants
adh (Sang et al. 1997)
argenine carboxylase (Galloway et al. 1998)
CRABS CLAW (CRC) (Oh and Manos 2008)
GBSSI (granule bound starch synthase) or waxy (Harbaugh 2008, Mason-Gamer et al. 1998,
Winkworth and Donoghue 2004)
glutamine synthetase (Emshwiller and Doyle 1999)
glycerol 3-phosphate acyltransferase (Tank and Sang 2001)
Hf1 (Chen et al. 2007)
histone H3 intron (Doyle et al. 1996)
LEAFY (Oh and Potter 2003)
malate synthase (Lewis and Doyle 2001)
NADP-dependent isocitrate dehydrogenase (IDH) (Weese and Johnson 2005)
nitrate reductase (Howarth and Baum 2002)
PEP carboxylase (Gaskin and Schaal 2002, Helfgott and Mason-Gamer 2004)
pgiC (Gottlieb and Ford 1996)
Phytochromes (Mathews et al. 1995)
pistillata (Bailey and Doyle 1999)
RNA polymerase II (RPB2) (Goetsch et al. 2005, Oxelman et al. 2004, Popp and Oxelman 2007,
Thomas et al. 2006)
sorbitol 6-phosphate dehydrogenase (Bortiri et al. 2002)
Reviews of the topic by (Sang 2002, Sang and Zhang 1999, Whittall et al. 2006)
Literature Cited
Bailey, C., and J. Doyle. 1999. Potential phylogenetic utility of the low-copy nuclear gene
pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in
Sphaerocardamum and other Brassicaceae. Mol Phylogenet Evol 13: 20-30.
Bortiri, E., S. Oh, F. Gao, and D. Potter. 2002. The phylogenetic utility of nucleotide sequences
of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae). Amer. J. Bot. 89: 16971708.
Chen, S. M., K. Matsubara, T. Omori, H. Kokubun, H. Kodama, H. Watanabe, G. Hashimoto, E.
Marchesi, L. Bullrich, and T. Ando. 2007. Phylogenetic analysis of the genus Petunia
(Solanaceae) based on the sequence of the Hf1 gene. Journal of Plant Research 120: 385397.
Doyle, J., V. Kanazin, and R. Shoemaker. 1996. Phylogenetic utility of histone H3 intron
sequences in the perennial relatives of soybean (Glycine: Leguminosae). Mol Phylogenet
Evol 6: 438-447.
Emshwiller, E., and J. Doyle. 1999. Chloroplast-expressed glutamine synthetase (ncpGS):
potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae). Mol
Phylogenet Evol 12(3): 310-319.
Galloway, G., R. Malmberg, and R. Price. 1998. Phylogenetic utility of the nuclear gene arginine
decarboxylase: An example from Brassicaceae. Mol. Biol. Evol. 15: 1312-1320.
Gaskin, J. F., and B. A. Schaal. 2002. Hybrid Tamarix widespread in U.S. invasion and
undetected in native Asian range. Proc. Natl. Acad. Sci. USA 99: 11256-11259.
Goetsch, L., A. J. Eckert, and B. D. Hall. 2005. The molecular systematics of Rhododendron
(Ericaceae): A phylogeny based upon RPB2 gene sequences. Systematic Botany 30: 616626.
Gottlieb, L., and V. Ford. 1996. Phylogenetic relationships among the sections of Clarkia
(Onagraceae) inferred from the nucleotide sequences of PgiC. Systematic Botany 21: 4562.
Harbaugh, D. T. 2008. Polyploid and hybrid origins of pacific island sandalwoods (Santalum,
Santalaceae) inferred from low-copy nuclear and flow cytometry data. International
Journal of Plant Sciences 169: 677-685.
Helfgott, D. M., and R. J. Mason-Gamer. 2004. The evolution of North American Elymus
(Triticeae, Poaceae) allotetraploids: Evidence from phosphoenolpyruvate carboxylase
gene sequences. Systematic Botany 29: 850-861.
Howarth, D. G., and B. A. Baum. 2002. Phylogenetic utility of a nuclear intron from nitrate
reductase for the study of closely related plant species. Mol Phylogenet Evol 23: 525-528.
Lewis, C., and J. Doyle. 2001. Phylogenetic utility of the nuclear gene malate synthase in the
palm family (Arecaceae). Mol. Phylogenet. Evol. 19: 409-420.
Mason-Gamer, R., C. Weil, and E. Kellogg. 1998. Granule-bound starch synthase: structure,
function, and phylogenetic utility. Mol Biol Evol 15: 1658-1673.
Mathews, S., M. Lavin, and R. A. Sharrock. 1995. Evolution of the phytochrome gene family
and Its utility for phylogenetic analyses of angiosperms. Annals of the Missouri Botanical
Garden 82: 296-321.
Oh, S.-H., and P. S. Manos. 2008. Molecular phylogenetics and cupule evolution in Fagaceae as
inferred from nuclear CRABS CLAW sequences. Taxon 57: 434-451.
Oh, S. H., and D. Potter. 2003. Phylogenetic utility of the second intron of LEAFY in Neillia and
Stephanandra (Rosaceae) and implications for the origin of Stephanandra. Molecular
Phylogenetics and Evolution 29: 203-215.
Oxelman, B., N. Yoshikawa, B. McConaughy, J. Lou, A. Denton, and B. D. Hall. 2004. Rpb2
gene phylogeny in flowering plants, with particular emphasis on asterids. Mol Phylogenet
Evol. 32: 462-479.
Popp, M., and B. Oxelman. 2007. Origin and evolution of North American polyploid Silene
(Caryophyllaceae). American Journal of Botany 94: 330-349.
Sang, T. 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Critical
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Sang, T., M. J. Donoghue, and D. Zhang. 1997. Evolution of alcohol dehdrogenase genes in
peonies (Paeonia): phylogenetic relationships of putative nonhybrid species. Mol.
Phylog. Evol. 14: 994-1007.
Sang, T., and D. Zhang. 1999. Reconstructing hybrid speciation using sequences of low copy
nuclear genes: Hybrid origins of five Paeonia species based on Adh gene phylogenies.
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Tank, D., and T. Sang. 2001. Phylogenetic utility of the glycerol-3-phosphate acyltransferase
gene: evolution and implications in Paeonia (Paeoniaceae). Molecular Phylogenetics And
Evolution 19: 421-429.
Thomas, M. M., N. C. Garwood, W. J. Baker, S. A. Henderson, S. J. Russell, D. R. Hodel, and
R. M. Bateman. 2006. Molecular phylogeny of the palm genus Chamaedorea, based on
the low-copy nuclear genes PRK and RPB2. Molecular Phylogenetics and Evolution 38:
398-415.
Weese, T. L., and L. A. Johnson. 2005. Utility of NADP-dependent isocitrate dehydrogenase for
species-level evolutionary inference in angiosperm phylogeny: a case study in Saltugilia.
Mol Phylogenet Evol. 36: 24--41.
Whittall, J. B., A. Medina-Marino, E. A. Zimmer, and S. A. Hodges. 2006. Generating singlecopy nuclear gene data for a recent adaptive radiation. Molecular Phylogenetics and
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Winkworth, R. C., and M. J. Donoghue. 2004. Viburnum phylogeny: evidence from the
duplicated nuclear gene GBSSI. Molecular Phylogenetics and Evolution 33: 109-126.
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