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Studies of flower development in core eudicot species have established a central role for B class MADS-box genes in specifying petal and stamen identities. Similarly in maize and rice, B class genes are essential for Iodicule and stamen specification, suggesting homology of petals and Iodicules and conservation of B class gene activity across angiosperms. However, Iodicules are grass-specific organs with a morphology distinct from petals, thus their true homology to eudicot and nongrass monocot floral organs has been a topic of debate. To understand the relationship of Iodicules to the sterile floral organs of nongrass monocots we have isolated and observed the expression of B class genes from a basal grass Streptochaeta that diverged before the evolution of Iodicules, as well as the outgroups Joinvillea and Elegia, which have a typical monocot floral plan. Our results support a conserved role for B function genes across the angiosperms and provide additional evidence linking the evolution of Iodicules and second whorl tepal/petals of monocots. The expression data and morphological analysis suggest that the function of B class genes should be broadly interpreted as required for differentiation of a distinct second floral whorl as opposed to specifying petal identity per se. flower development | MADS-box | petal evolution | B-function | Streptochaeta

Angiosperms provide much of our food, fibre, medicine and timber, although their origin and early evolution have remained enigmatic. A phylogentic analysis of DNA sequences of five mitochondrial, plastid and nuclear genes is reported, showing that Amborella, Nymphaeales and Illiciales-Trimeniaceae-Austrobaileya are the first stage of angiosperm evolution.

Abstract Background Members of the cation diffusion facilitator (CDF) family are integral membrane divalent cation transporters that transport metal ions out of the cytoplasm either into the extracellular space or into internal compartments such as the vacuole. The spectrum of cations known to be transported by proteins of the CDF family include Zn, Fe, Co, Cd, and Mn. Members of this family have been identified in prokaryotes, eukaryotes, and archaea, and in sequenced plant genomes. CDF families range in size from nine members in Selaginella moellendorffii to 19 members in Populus trichocarpa. Phylogenetic analysis suggests that the CDF family has expanded within plants, but a definitive plant CDF family phylogeny has not been constructed. Results Representative CDF members were annotated from diverse genomes across the Viridiplantae and Rhodophyta lineages and used to identify phylogenetic relationships within the CDF family. Bayesian phylogenetic analysis of CDF amino acid sequence data supports organizing land plant CDF family sequences into 7 groups. The origin of the 7 groups predates the emergence of land plants. Among these, 5 of the 7 groups are likely to have originated at the base of the tree of life, and 2 of 7 groups appear to be derived from a duplication event prior to or coincident with land plant evolution. Within land plants, local expansion continues within select groups, while several groups are strictly maintained as one gene copy per genome. Conclusions Defining the CDF gene family phylogeny contributes to our understanding of this family in several ways. First, when embarking upon functional studies of the members, defining primary groups improves the predictive power of functional assignment of orthologous/paralogous genes and aids in hypothesis generation. Second, defining groups will allow a group-specific sequence motif to be generated that will help define future CDF family sequences and aid in functional motif identification, which currently is lacking for this family in plants. Third, the plant-specific expansion resulting in Groups 8 and 9 evolved coincident to the early primary radiation of plants onto land, suggesting these families may have been important for early land colonization.

Relationships among core eudicot clades (the asterid, rosid, Caryophyllales, Santalales, Berberidopsidales, and Myrothamnaceae/Gunneraceae clades) remain one of the last major questions of deep-level phylogeny in the angiosperms. To resolve these relationships, we assembled a large data set of entire 26S ribosomal DNA sequences for approximately 250 angiosperms. The 26S rDNA is just under 3.4 kb in length and consists of conserved core areas, as well as more rapidly evolving expansion segments. Because of is length and regions with different evolutionary rates, it appears to be highly useful for resolving relationships at this level. We constructed several different data sets and analyzed them using parsimony: 1) 26S rDNA sequences were added to the existing 567-taxon matrix (Soltis et al.), 2) a smaller data set was constructed for only those angiosperms for which all four genes were available. We also used a compartmentalization approach, reconstructing ancestral sequences for major clades. Our preliminary analyses provide additional support for the major core eudicot clades and the relationships of early-branching eudicots.

The most comprehensive phylogenetic study of monocotyledons based on DNA sequences includes 100 of the 102 currently recognized families (APG 1998) and is based on a combined analysis of rbcL, atpB, and 18S (Chase et al. 2000). This phylogeny is well resolved and well supported, except for the higher level inter-relationships among some orders. Separate analyses of the plastid genes, rbcL and atpB, result in well resolved strict consensus trees, whereas an analysis of the nuclear 18S gene gives a far less resolved consensus tree. Furthermore, the composition of a number of clades in the 18S topology differs from those of the plastid gene topologies. It is therefore important to add another nuclear DNA region to the three-gene data set, to gain further confirmation for the plastid DNA topologies and higher bootstrap support for the ordinal clades. Only a few studies have used the 3400 base pair long 26S gene for cladistic analyses, and we explore the phylogenetic information from this nuclear ribosomal DNA region. The results presented are based on the first 1200 base pairs, which contain six of the 12 expansion segments. These sequences could be aligned easily across monocot families, except for a few highly variable areas of the expansion segments. The 26S region produced about the same number of parsimony informative characters as rbcL and atpB, and more informative characters than 18S. The strict consensus tree resulting from cladistic analysis of 26S sequences is comparable to the well resolved strict consensus trees of rbcL and atpB, and much better resolved than the 18S consensus tree. The 26S topology largely recovered the clades present in the previous analyses of rbcL, atpB, and combined rbcL, atpB, and 18S. Many smaller clades received high bootstrap support, but most major clades had less than 50% support.

DNA sequences of nine genes (plastid: atpB, matK, and rbcL; mitochondrial: atp1, matR, mtSSU, and mtLSU; nuclear: 18S and 26S rDNAs) from 100 species of basal angiosperms and gymnosperms were analyzed using parsimony, Bayesian, and maximum likelihood methods. All of these analyses support the following consensus of relationships among basal angiosperms. First, Amborella, Nymphaeaceae, and Austrobaileyales are strongly supported as a basal grade in the angiosperm phylogeny, with either Amborella or Amborella and Nymphaeales as sister to all other angiosperms. An examination of nucleotide substitution patterns of all nine genes ruled out any possibility of analytical artifacts because of RNA editing and GC-content bias in placing these taxa at the base of the angiosperm phylogeny. Second, Magnoliales are sister to Laurales and Piperales are sister to Canellales. These four orders together constitute the magnoliid clade. Finally, the relationships among Ceratophyllum, Chloranthaceae, monocots, magnoliids, and eudicots are resolved in different ways in various analyses, mostly with low support. Our study indicates caution in total evidence approaches in that some of the genes employed (e.g., mtSSU, mtLSU, and nuclear 26S rDNA) added signal that conflicted with the other genes in resolving certain parts of the phylogenetic tree. [ABSTRACT FROM AUTHOR]

A correction to the article "Comparative Analysis of Complete Chloroplast Genome Sequence and Inversion Variation in Lasthenia Burkei (Madieae, Asteraceae)" that was published in the April 2014 issue is presented.