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Table 3
Taxa included phylogenetic analyses with GenBank accession numbers and references. Taxa in bold are those which have not appeared in any previous phylogenetic studies using 61 genes from complete chloroplast genome sequences.
Taxon	GenBank Accession Numbers	Reference

Gymnosperms –Outgroups
Pinus thunbergii	NC_001631	Wakasugi et al. 1994 [72]
Ginkgo biloba	DQ069337–DQ069702	Leebens-Mack et al 2005 [27]
Basal Angiosperms
Amborella trichopoda	NC_005086	Goremykin et al. 2003 [29]
Nuphar advena	DQ069337–DQ069702	Leebens-Mack et al 2005 [27]
Nymphaea alba	NC_006050	Goremykin et al. 2004 [28]
Monocots
Acorus americanus	DQ069337–DQ069702	Leebens-Mack et al 2005 [27]
Oryza sativa	NC_001320	Hiratsuka et al. 1989 [73]
Saccharum officinarum	NC_006084	Asano et al. 2004 [74]
Triticum aestivum	NC_002762	Ikeo and Ogihara, unpublished
Typha latifolia	DQ069337–DQ069702	Leebens-Mack et al 2005 [27]
Yucca schidigera	DQ069337–DQ069702	Leebens-Mack et al 2005 [27]
Zea mays	NC_001666	Maier et al. 1995 [75]
Magnoliids
Calycanthus floridus	NC_004993	Goremykin et al. 2003 [76]
Eudicots
Arabidopsis thalliana	NC_000932	Sato et al. 1999 [77]
Atropa belladonna	NC_004561	Schmitz-Linneweber et al. 2002 [53]
*Cucumis sativus*	NC_007144	Plader et al. unpublished
*Eucalyptus globulus*	AY780259	Steane 2005 [78]
*Glycine max*	DQ317523	Saski et al. 2005 [3]
*Gossypium hirsutum*	DQ345959	Current study
Lotus corniculatus	NC_002694	Kato et al. 2000 [79]
Medicago truncatula	NC_003119	Lin et al., unpublished
Nicotiana tabacum	NC_001879	Shinozaki et al. 1986 [80]
Oenothera elata	NC_002693	Hupfer et al. 2000 [81]
Panax schinseng	NC_006290	Kim and Lee 2004 [82]
Ranunculus macranthus	DQ069337–DQ069702	Leebens-Mack et al 2005 [27]
*Solanum lycopersicum*	DQ347959	Daniell et al. in press
*Solanum bulboscastanum*	DQ347958	Daniell et al. in press
Spinacia oleracea	NC_002202	Schmitz-Linneweber et al. 2001 [83]

Lee et al. BMC Genomics 2006 7:61 doi:10.1186/1471-2164-7-61

Table 3