Richard G. Olmstead

Mark W. Chase, Douglas E. Soltis, Richard G. Olmstead, David Morgan, Donald H. Les, Brent D. Mishler, Melvin R. Duvall, Robert A. Price, Harold G. Hills, Yin-Long Qiu, Kathleen A. Kron, Jeffrey H. Rettig, Elena Conti, Jeffrey D. Palmer, James R. Manhart, Kenneth J. Sytsma, Helen J. Michaels, W. John Kress, Kenneth G. Karol, W. Dennis Clark, Mikael Hedren, Brandon S. Gaut, Robert K. Jansen, Ki-Joong Kim, Charles F. Wimpee, James F. Smith, Glenn R. Furnier, Steven H. Strauss, Qui-Yun Xiang, Gregory M. Plunkett, Pamela S. Soltis, Susan M. Swensen, Stephen E. Williams, Paul A. Gadek, Christopher J. Quinn, Luis E. Eguiarte, Edward Golenberg, Gerald H. Learn, Jr., Sean W. Graham, Spencer C. H. Barrett, Selvadurai Dayanandan, Victor A. Albert, Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL, Annals of the Missouri Botanical Garden, Vol. 80, No. 3 (1993), pp. 528-548+550-580

Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.

PREMISE OF THE STUDY: Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS: We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS: Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS: Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.