The nuclear gene xanthine dehydrogenase (Xdh) was sequenced for 247 genera representing all major lineages of angiosperms and “gymnosperms,” and the results were analyzed using likelihood and parsimony methods. The overall topology is mostly congruent with previously published trees based on chloroplast rbcL, atpB, and matK sequences. A total of 190 of the 253 nodes (71%) of the Xdh tree received bootstrap support greater than 50%. The likelihood tree was comparable in robustness to the matK topology, which exhibited 79% of the nodes with bootstrap support greater than 50%, and to the reported 7%–24% support observed for individual analyses of rbcL, atpB, and 18S ribosomal DNA clades. The number of parsimony-informative sites (1068, 69%) was similar to that of the matK (1083, 62%) study. The likelihood tree depicts angiosperms as monophyletic, with Ceratophyllum L. (Ceratophyllaceae) as sister to the rest of the flowering plants, followed successively by Amborellaceae, Nymphaeaceae, and Austrobaileyales clades as sisters to the remaining angiosperms. Acorus L. plus the remaining monocots, magnoliids, and Chloranthaceae diverge after the Austrobaileyales. Eudicots are supported and include a basal grade of Ranunculales–Proteaceae, Sabiaceae, Trochodendraceae, Buxaceae, Gunneraceae, and Dilleniaceae–Santalaceae, which are subsequent sister to the remaining eudicots. The remaining eudicots are split into two clades. The first clade consists of the Ericales, Cornales, and euasterids I and II (lamids–campanulids). The second clade consists of the following orders: Saxifragales, Myrtales–Caryophyllales–Cucurbitales, Crossosomatales, Geraniales, Rosales–Fabales–Fagales, Celastrales, Malpighiales, Brassicales–Malvales, Oxalidales, and Sapindales. Xdh data provided good support in the Caryophyllales, Ericales and Cornales, euasterids I (lamids), Magnoliales and Laurales, Malvales, Rutaceae, Oxalidales, Brassicales, and Sapindales. A future combined analysis of Xdh and other DNA data sets will have a strong potential to enhance resolution and internal support for angiosperm phylogenetics and provide insights into angiosperm evolution using biparental information.
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